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_2686906.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2686906.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2686906.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.53, per 1000 atoms: 0.45 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: 0.50 Conformation dependent library (CDL) restraints added in 169.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 531 0.91 - 1.16: 1106 1.16 - 1.41: 612 1.41 - 1.66: 849 1.66 - 1.91: 55 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.117 0.209 1.10e-02 8.26e+03 3.63e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.449 0.088 5.00e-03 4.00e+04 3.07e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.409 -0.173 9.90e-03 1.02e+04 3.06e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.237 1.029 0.208 1.19e-02 7.06e+03 3.04e+02 bond pdb=" N PRO A 43 " pdb=" CD PRO A 43 " ideal model delta sigma weight residual 1.473 1.240 0.233 1.40e-02 5.10e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 3001 4.29 - 8.58: 1829 8.58 - 12.86: 754 12.86 - 17.15: 172 17.15 - 21.44: 21 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.83 108.11 12.72 5.90e-01 2.87e+00 4.65e+02 angle pdb=" O LYS A 148 " pdb=" C LYS A 148 " pdb=" N ASP A 149 " ideal model delta sigma weight residual 123.31 104.50 18.81 1.17e+00 7.31e-01 2.58e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 109.20 10.09 6.50e-01 2.37e+00 2.41e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.52 120.04 -9.52 6.70e-01 2.23e+00 2.02e+02 angle pdb=" O GLY A 137 " pdb=" C GLY A 137 " pdb=" N HIS A 138 " ideal model delta sigma weight residual 122.51 133.94 -11.43 8.10e-01 1.52e+00 1.99e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 1309 17.02 - 34.04: 120 34.04 - 51.06: 36 51.06 - 68.08: 13 68.08 - 85.10: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 172 " pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" CB LEU A 172 " ideal model delta harmonic sigma weight residual -122.60 -140.71 18.11 0 2.50e+00 1.60e-01 5.25e+01 dihedral pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CA LEU A 172 " pdb=" CB LEU A 172 " ideal model delta harmonic sigma weight residual 122.80 139.11 -16.31 0 2.50e+00 1.60e-01 4.26e+01 dihedral pdb=" N AASN A 76 " pdb=" C AASN A 76 " pdb=" CA AASN A 76 " pdb=" CB AASN A 76 " ideal model delta harmonic sigma weight residual 122.80 106.88 15.92 0 2.50e+00 1.60e-01 4.05e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.197: 98 0.197 - 0.393: 74 0.393 - 0.588: 50 0.588 - 0.784: 17 0.784 - 0.979: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 172 " pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CB LEU A 172 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " 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 ALA A 111 " pdb=" N ALA A 111 " pdb=" C ALA A 111 " pdb=" CB ALA A 111 " both_signs ideal model delta sigma weight residual False 2.48 3.35 -0.86 2.00e-01 2.50e+01 1.86e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.114 2.00e-02 2.50e+03 6.83e-02 1.40e+02 pdb=" CG TYR A 141 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.126 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.073 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.081 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.028 2.00e-02 2.50e+03 6.07e-02 1.11e+02 pdb=" CG PHE A 164 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.081 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.114 2.00e-02 2.50e+03 6.03e-02 1.09e+02 pdb=" CG PHE A 119 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.098 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.063 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.016 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.007 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 828 2.29 - 2.87: 7894 2.87 - 3.44: 10636 3.44 - 4.02: 15268 4.02 - 4.60: 21897 Nonbonded interactions: 56523 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.711 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.751 2.450 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.823 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.851 2.450 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.852 2.450 ... (remaining 56518 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_2686906_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= 0.3625 r_free= 0.2050 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.476502 | | target function (ml) not normalized (work): 22069.157249 | | target function (ml) not normalized (free): 1149.018454 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3804 0.2244 4.8561 4.9083| | 2: 3.78 - 3.00 1.00 2430 110 0.3407 0.1724 4.0859 4.1094| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 6617.51| | 2: 3.78 - 3.00 2430 110 0.94 11.36 1.48 0.26 458.88| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 390.34 max = 12078.24 mean = 3581.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.37| |phase err.(test): min = 0.00 max = 89.98 mean = 33.32| |-----------------------------------------------------------------------------| ----------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 0.248 1557 Z= 5.529 Angle : 5.240 18.808 2118 Z= 3.762 Chirality : 0.353 0.979 243 Planarity : 0.034 0.118 284 Dihedral : 13.585 85.097 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 27.03 % 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: -3.08 (0.48), residues: 224 helix: -2.85 (0.38), residues: 109 sheet: -1.23 (0.83), residues: 28 loop : -0.84 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.017 ARG A 98 TYR 0.136 0.046 TYR A 141 PHE 0.093 0.046 PHE A 119 HIS 0.062 0.030 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= 0.3625 r_free= 0.2050 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.476502 | | target function (ml) not normalized (work): 22069.157249 | | target function (ml) not normalized (free): 1149.018454 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3579 0.3657 0.2133 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3579 0.3657 0.2133 n_refl.: 5182 remove outliers: r(all,work,free)=0.2535 0.2559 0.2133 n_refl.: 5178 overall B=-2.84 to atoms: r(all,work,free)=0.2428 0.2449 0.2089 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1579 0.1580 0.1580 n_refl.: 5178 remove outliers: r(all,work,free)=0.1575 0.1575 0.1580 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 0.3737 449.646 411.102 0.677 1.044 0.398 11.894-9.307 99.02 97 4 0.1900 714.299 691.918 0.958 1.043 0.383 9.237-7.194 100.00 213 7 0.2234 584.155 576.647 0.986 1.039 0.354 7.162-5.571 100.00 427 22 0.2344 438.337 424.155 0.952 1.030 0.316 5.546-4.326 100.00 867 58 0.1413 601.775 594.711 0.990 1.016 0.278 4.315-3.360 100.00 1859 96 0.1321 572.295 566.490 1.050 0.993 0.168 3.356-3.002 100.00 1373 60 0.1606 440.805 432.885 1.049 0.970 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6263 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1575 r_free=0.1580 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=0.1576 r_free=0.1588 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 20.048745 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.993078 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 0.1168 0.1821 0.0652 0.010 1.0 2.9 0.5 0.0 0 10.024 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.68 18.21 6.52 3.013 16.022 1.993 0.018 10.25 18.00 7.75 4.908 16.181 1.993 0.015 Individual atomic B min max mean iso aniso Overall: 2.16 111.46 17.35 5.31 1785 0 Protein: 2.16 111.41 14.65 5.30 1519 0 Water: 4.03 111.46 33.05 N/A 258 0 Other: 16.87 37.42 24.18 N/A 8 0 Chain A: 2.16 111.46 17.35 N/A 1785 0 Histogram: Values Number of atoms 2.16 - 13.09 919 13.09 - 24.02 484 24.02 - 34.95 187 34.95 - 45.88 109 45.88 - 56.81 55 56.81 - 67.74 14 67.74 - 78.67 8 78.67 - 89.60 5 89.60 - 100.53 1 100.53 - 111.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1025 r_free=0.1800 r_work=0.1019 r_free=0.1810 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1019 r_free = 0.1810 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 = 0.1016 r_free = 0.1802 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 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= 0.1016 r_free= 0.1802 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014042 | | target function (ls_wunit_k1) not normalized (work): 69.141257 | | target function (ls_wunit_k1) not normalized (free): 10.657329 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1057 0.1016 0.1802 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2087 0.2086 0.2221 n_refl.: 5176 remove outliers: r(all,work,free)=0.2087 0.2086 0.2221 n_refl.: 5176 overall B=-0.94 to atoms: r(all,work,free)=0.2048 0.2046 0.2211 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1053 0.1014 0.1788 n_refl.: 5176 remove outliers: r(all,work,free)=0.1053 0.1014 0.1788 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 0.3296 330.566 312.621 0.670 1.014 0.381 11.894-9.307 99.02 97 4 0.1565 525.130 515.810 0.977 1.015 0.361 9.237-7.194 100.00 213 7 0.1664 429.452 429.471 1.014 1.014 0.315 7.162-5.571 100.00 427 22 0.1596 322.252 319.077 0.978 1.011 0.302 5.546-4.326 100.00 867 58 0.0925 442.406 438.975 0.996 1.006 0.242 4.315-3.360 100.00 1859 96 0.0765 420.733 420.748 1.042 0.998 0.186 3.356-3.002 100.00 1373 60 0.1001 324.066 322.506 1.017 0.990 0.089 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3743 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1014 r_free=0.1788 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=0.1016 r_free=0.1788 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1016 r_free=0.1788 | n_water=258 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.1041 r_free=0.1784 | n_water=247 | time (s): 20.360 (total time: 20.860) Filter (q & B) r_work=0.1042 r_free=0.1785 | n_water=244 | time (s): 1.290 (total time: 22.150) Compute maps r_work=0.1042 r_free=0.1785 | n_water=244 | time (s): 0.460 (total time: 22.610) Filter (map) r_work=0.1352 r_free=0.1850 | n_water=141 | time (s): 1.480 (total time: 24.090) Find peaks r_work=0.1352 r_free=0.1850 | n_water=141 | time (s): 0.480 (total time: 24.570) Add new water r_work=0.1689 r_free=0.2156 | n_water=224 | time (s): 1.220 (total time: 25.790) Refine new water occ: r_work=0.1151 r_free=0.1657 adp: r_work=0.1134 r_free=0.1663 occ: r_work=0.1131 r_free=0.1633 adp: r_work=0.1123 r_free=0.1643 occ: r_work=0.1123 r_free=0.1625 adp: r_work=0.1123 r_free=0.1625 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1625 r_work=0.1123 r_free=0.1625 | n_water=224 | time (s): 3.350 (total time: 29.140) Filter (q & B) r_work=0.1123 r_free=0.1630 | n_water=223 | time (s): 1.370 (total time: 30.510) Filter (dist only) r_work=0.1130 r_free=0.1605 | n_water=219 | time (s): 16.920 (total time: 47.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 20.851735 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.902666 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 0.1028 0.1741 0.0714 0.009 0.9 3.8 0.5 0.6 0 10.426 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.28 17.41 7.14 4.671 16.599 2.903 0.014 9.53 17.82 8.30 5.706 17.122 2.903 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.65 16.52 6.80 1746 0 Protein: 0.00 107.65 15.19 6.78 1519 0 Water: 0.00 62.80 25.40 N/A 219 0 Other: 11.10 37.95 25.17 N/A 8 0 Chain A: 0.00 107.65 15.92 N/A 1665 0 Chain S: 3.88 60.54 28.73 N/A 81 0 Histogram: Values Number of atoms 0.00 - 10.76 682 10.76 - 21.53 646 21.53 - 32.29 231 32.29 - 43.06 118 43.06 - 53.82 32 53.82 - 64.59 24 64.59 - 75.35 6 75.35 - 86.12 3 86.12 - 96.88 2 96.88 - 107.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.0953 r_free=0.1782 r_work=0.0949 r_free=0.1784 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0949 r_free = 0.1784 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0947 r_free = 0.1777 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 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= 0.0947 r_free= 0.1777 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ls_wunit_k1) (work): 0.012152 | | target function (ls_wunit_k1) not normalized (work): 59.836337 | | target function (ls_wunit_k1) not normalized (free): 9.783099 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0988 0.0947 0.1777 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2171 0.2182 0.2166 n_refl.: 5176 remove outliers: r(all,work,free)=0.2171 0.2182 0.2166 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2171 0.2182 0.2166 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0992 0.0952 0.1776 n_refl.: 5176 remove outliers: r(all,work,free)=0.0989 0.0948 0.1776 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 0.3115 329.962 311.363 0.662 1.009 0.354 11.894-9.307 99.02 97 4 0.1491 525.130 515.641 0.983 1.011 0.350 9.237-7.194 100.00 213 7 0.1429 429.452 428.435 1.016 1.011 0.314 7.162-5.571 100.00 427 22 0.1466 322.252 317.854 0.997 1.009 0.300 5.546-4.326 100.00 867 58 0.0806 442.406 439.025 1.013 1.005 0.260 4.315-3.360 100.00 1859 96 0.0738 420.733 421.009 1.065 0.999 0.200 3.356-3.002 100.00 1373 60 0.0978 324.066 324.281 1.044 0.993 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-4.6144 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0948 r_free=0.1776 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0950 r_free=0.1774 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0950 r_free=0.1774 | n_water=219 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0967 r_free=0.1786 | n_water=215 | time (s): 16.730 (total time: 17.270) Filter (q & B) r_work=0.1027 r_free=0.1849 | n_water=213 | time (s): 1.770 (total time: 19.040) Compute maps r_work=0.1027 r_free=0.1849 | n_water=213 | time (s): 0.590 (total time: 19.630) Filter (map) r_work=0.1283 r_free=0.1882 | n_water=144 | time (s): 1.470 (total time: 21.100) Find peaks r_work=0.1283 r_free=0.1882 | n_water=144 | time (s): 0.490 (total time: 21.590) Add new water r_work=0.1676 r_free=0.2248 | n_water=233 | time (s): 1.180 (total time: 22.770) Refine new water occ: r_work=0.1063 r_free=0.1732 adp: r_work=0.1057 r_free=0.1735 occ: r_work=0.1044 r_free=0.1715 adp: r_work=0.1045 r_free=0.1725 occ: r_work=0.1033 r_free=0.1704 adp: r_work=0.1033 r_free=0.1714 ADP+occupancy (water only), MIN, final r_work=0.1033 r_free=0.1714 r_work=0.1033 r_free=0.1714 | n_water=233 | time (s): 11.590 (total time: 34.360) Filter (q & B) r_work=0.1034 r_free=0.1723 | n_water=231 | time (s): 1.720 (total time: 36.080) Filter (dist only) r_work=0.1044 r_free=0.1728 | n_water=229 | time (s): 19.200 (total time: 55.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.130728 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.259514 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 0.0939 0.1827 0.0888 0.011 1.1 3.8 0.5 0.6 0 0.565 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.39 18.27 8.88 5.630 18.044 0.260 5.167 8.97 18.45 9.48 7.602 18.105 0.260 5.072 Individual atomic B min max mean iso aniso Overall: 0.00 107.22 16.65 9.45 1756 0 Protein: 0.00 107.22 15.41 9.44 1519 0 Water: 0.00 57.80 24.51 N/A 229 0 Other: 11.16 42.53 27.39 N/A 8 0 Chain A: 0.00 107.22 16.10 N/A 1650 0 Chain S: 0.00 49.91 25.19 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.72 664 10.72 - 21.44 643 21.44 - 32.17 259 32.17 - 42.89 112 42.89 - 53.61 45 53.61 - 64.33 14 64.33 - 75.05 9 75.05 - 85.78 5 85.78 - 96.50 4 96.50 - 107.22 1 =========================== Idealize ADP of riding H ========================== r_work=0.0897 r_free=0.1845 r_work=0.0903 r_free=0.1855 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0903 r_free = 0.1855 target_work(ml) = 5.077 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0891 r_free = 0.1844 target_work(ml) = 5.070 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0891 r_free= 0.1844 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.070422 | | target function (ml) not normalized (work): 24956.618778 | | target function (ml) not normalized (free): 1852.524385 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0939 0.0891 0.1844 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2080 0.2087 0.2109 n_refl.: 5174 remove outliers: r(all,work,free)=0.2080 0.2087 0.2109 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2080 0.2087 0.2109 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0886 0.1845 n_refl.: 5174 remove outliers: r(all,work,free)=0.0934 0.0886 0.1845 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 0.3553 329.962 305.382 0.626 0.990 0.340 11.894-9.307 99.02 97 4 0.1797 525.130 510.506 0.952 0.995 0.340 9.237-7.194 100.00 213 7 0.1804 429.452 424.170 0.993 0.997 0.300 7.162-5.571 100.00 427 22 0.1832 322.252 312.624 0.979 0.998 0.292 5.546-4.326 100.00 867 58 0.0913 442.406 437.110 0.994 1.000 0.250 4.315-3.360 100.00 1859 96 0.0605 420.733 420.253 1.050 1.003 0.210 3.356-3.002 100.00 1373 60 0.0602 324.066 323.807 1.026 1.005 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.1546 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0886 r_free=0.1845 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0886 r_free=0.1845 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0886 r_free=0.1845 | n_water=229 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.0916 r_free=0.1872 | n_water=223 | time (s): 18.680 (total time: 19.370) Filter (q & B) r_work=0.0985 r_free=0.1873 | n_water=219 | time (s): 1.960 (total time: 21.330) Compute maps r_work=0.0985 r_free=0.1873 | n_water=219 | time (s): 0.630 (total time: 21.960) Filter (map) r_work=0.1245 r_free=0.1890 | n_water=147 | time (s): 1.550 (total time: 23.510) Find peaks r_work=0.1245 r_free=0.1890 | n_water=147 | time (s): 0.580 (total time: 24.090) Add new water r_work=0.1605 r_free=0.2254 | n_water=227 | time (s): 1.780 (total time: 25.870) Refine new water occ: r_work=0.1029 r_free=0.1812 adp: r_work=0.1025 r_free=0.1828 occ: r_work=0.1014 r_free=0.1805 adp: r_work=0.1014 r_free=0.1813 occ: r_work=0.1004 r_free=0.1789 adp: r_work=0.1004 r_free=0.1799 ADP+occupancy (water only), MIN, final r_work=0.1004 r_free=0.1799 r_work=0.1004 r_free=0.1799 | n_water=227 | time (s): 9.340 (total time: 35.210) Filter (q & B) r_work=0.1004 r_free=0.1800 | n_water=226 | time (s): 1.590 (total time: 36.800) Filter (dist only) r_work=0.1005 r_free=0.1779 | n_water=221 | time (s): 18.610 (total time: 55.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.073830 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.213471 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 0.1858 0.0940 0.011 1.1 4.8 0.5 0.6 0 0.537 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.18 18.58 9.40 7.318 18.259 0.213 5.071 8.93 18.64 9.71 8.277 18.338 0.213 5.010 Individual atomic B min max mean iso aniso Overall: 0.00 105.34 16.82 10.68 1748 0 Protein: 0.00 105.34 15.74 10.67 1519 0 Water: 0.00 58.73 23.80 N/A 221 0 Other: 12.96 45.94 28.74 N/A 8 0 Chain A: 0.00 105.34 16.34 N/A 1638 0 Chain S: 0.00 58.73 24.03 N/A 110 0 Histogram: Values Number of atoms 0.00 - 10.53 644 10.53 - 21.07 631 21.07 - 31.60 273 31.60 - 42.14 110 42.14 - 52.67 54 52.67 - 63.21 15 63.21 - 73.74 9 73.74 - 84.28 5 84.28 - 94.81 4 94.81 - 105.34 3 =========================== Idealize ADP of riding H ========================== r_work=0.0893 r_free=0.1864 r_work=0.0897 r_free=0.1869 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1869 target_work(ml) = 5.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0886 r_free = 0.1859 target_work(ml) = 5.006 | | 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.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0886 r_free= 0.1859 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.006136 | | target function (ml) not normalized (work): 24640.198943 | | target function (ml) not normalized (free): 1977.883786 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0886 0.1859 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2133 0.2138 0.2188 n_refl.: 5174 remove outliers: r(all,work,free)=0.2133 0.2138 0.2188 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2133 0.2138 0.2188 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0885 0.1858 n_refl.: 5174 remove outliers: r(all,work,free)=0.0934 0.0885 0.1858 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 0.3533 329.962 304.799 0.630 0.991 0.334 11.894-9.307 99.02 97 4 0.1945 525.130 510.010 0.950 0.995 0.330 9.237-7.194 100.00 213 7 0.2076 429.452 422.586 0.991 0.998 0.288 7.162-5.571 100.00 427 22 0.1935 322.252 313.017 0.986 0.999 0.273 5.546-4.326 100.00 867 58 0.0975 442.406 436.507 1.002 1.000 0.240 4.315-3.360 100.00 1859 96 0.0581 420.733 420.096 1.068 1.002 0.210 3.356-3.002 100.00 1373 60 0.0485 324.066 323.813 1.049 1.003 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0054 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0885 r_free=0.1858 After: r_work=0.0888 r_free=0.1856 ================================== NQH flips ================================== r_work=0.0888 r_free=0.1856 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0888 r_free=0.1856 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0888 r_free=0.1856 | n_water=221 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0903 r_free=0.1864 | n_water=218 | time (s): 18.200 (total time: 18.740) Filter (q & B) r_work=0.0976 r_free=0.1866 | n_water=216 | time (s): 1.370 (total time: 20.110) Compute maps r_work=0.0976 r_free=0.1866 | n_water=216 | time (s): 0.540 (total time: 20.650) Filter (map) r_work=0.1232 r_free=0.1889 | n_water=160 | time (s): 1.300 (total time: 21.950) Find peaks r_work=0.1232 r_free=0.1889 | n_water=160 | time (s): 0.390 (total time: 22.340) Add new water r_work=0.1507 r_free=0.2167 | n_water=229 | time (s): 1.170 (total time: 23.510) Refine new water occ: r_work=0.0985 r_free=0.1870 adp: r_work=0.0979 r_free=0.1883 occ: r_work=0.0972 r_free=0.1866 adp: r_work=0.0971 r_free=0.1876 occ: r_work=0.0964 r_free=0.1857 adp: r_work=0.0963 r_free=0.1866 ADP+occupancy (water only), MIN, final r_work=0.0963 r_free=0.1866 r_work=0.0963 r_free=0.1866 | n_water=229 | time (s): 7.690 (total time: 31.200) Filter (q & B) r_work=0.0963 r_free=0.1864 | n_water=228 | time (s): 1.490 (total time: 32.690) Filter (dist only) r_work=0.0962 r_free=0.1848 | n_water=225 | time (s): 17.780 (total time: 50.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.968290 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.227776 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 0.0914 0.1887 0.0973 0.011 1.1 7.0 0.5 0.6 0 0.484 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.14 18.87 9.73 8.133 18.537 0.228 5.020 8.96 18.99 10.03 9.067 18.615 0.228 4.966 Individual atomic B min max mean iso aniso Overall: 0.00 103.93 17.07 11.95 1752 0 Protein: 0.00 103.93 16.05 11.93 1519 0 Water: 0.00 56.29 23.60 N/A 225 0 Other: 11.83 48.23 28.36 N/A 8 0 Chain A: 0.00 103.93 16.54 N/A 1633 0 Chain S: 0.00 53.38 24.36 N/A 119 0 Histogram: Values Number of atoms 0.00 - 10.39 600 10.39 - 20.79 652 20.79 - 31.18 273 31.18 - 41.57 127 41.57 - 51.96 62 51.96 - 62.36 16 62.36 - 72.75 7 72.75 - 83.14 8 83.14 - 93.54 5 93.54 - 103.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.0896 r_free=0.1899 r_work=0.0900 r_free=0.1904 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0900 r_free = 0.1904 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0891 r_free = 0.1894 target_work(ml) = 4.966 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0891 r_free= 0.1894 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.966154 | | target function (ml) not normalized (work): 24443.411212 | | target function (ml) not normalized (free): 2094.881328 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1261 0.1921 5.5331 6.2511| | 2: 3.78 - 3.00 1.00 2430 110 0.0441 0.1850 4.3848 10.975| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 12.06 1.00 0.99 13058.50| | 2: 3.78 - 3.00 2430 110 0.99 1.92 1.00 1.01 944.75| |alpha: min = 0.98 max = 1.01 mean = 1.00| |beta: min = 603.66 max = 21716.61 mean = 7077.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.88 mean = 7.06| |phase err.(test): min = 0.00 max = 88.03 mean = 7.52| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0942 0.0891 0.1894 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2158 0.2164 0.2189 n_refl.: 5174 remove outliers: r(all,work,free)=0.2158 0.2164 0.2189 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2158 0.2164 0.2189 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0941 0.0891 0.1893 n_refl.: 5174 remove outliers: r(all,work,free)=0.0941 0.0891 0.1893 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 0.3666 329.962 299.657 0.619 0.988 0.328 11.894-9.307 99.02 97 4 0.1880 525.130 512.706 0.965 0.992 0.327 9.237-7.194 100.00 213 7 0.2195 429.452 420.688 0.996 0.996 0.290 7.162-5.571 100.00 427 22 0.2057 322.252 311.310 0.992 0.997 0.290 5.546-4.326 100.00 867 58 0.1019 442.406 435.996 1.013 1.000 0.240 4.315-3.360 100.00 1859 96 0.0574 420.733 420.612 1.089 1.003 0.210 3.356-3.002 100.00 1373 60 0.0419 324.066 324.307 1.071 1.006 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9936 ================= 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 : 0.3625 0.2050 0.083 5.240 8.8 119.3 19.9 258 0.000 1_bss: 0.1575 0.1580 0.083 5.240 6.0 116.5 17.0 258 0.000 1_settarget: 0.1575 0.1580 0.083 5.240 6.0 116.5 17.0 258 0.000 1_nqh: 0.1576 0.1588 0.083 5.240 6.0 116.5 17.0 258 0.003 1_weight: 0.1576 0.1588 0.083 5.240 6.0 116.5 17.0 258 0.003 1_xyzrec: 0.1168 0.1821 0.010 1.000 6.0 116.5 17.0 258 0.204 1_adp: 0.1025 0.1800 0.010 1.000 2.2 111.5 17.4 258 0.204 1_regHadp: 0.1019 0.1810 0.010 1.000 2.2 111.5 17.4 258 0.204 1_occ: 0.1016 0.1802 0.010 1.000 2.2 111.5 17.4 258 0.204 2_bss: 0.1014 0.1788 0.010 1.000 1.2 110.5 16.4 258 0.204 2_settarget: 0.1014 0.1788 0.010 1.000 1.2 110.5 16.4 258 0.204 2_updatecdl: 0.1014 0.1788 0.010 1.030 1.2 110.5 16.4 258 0.204 2_nqh: 0.1016 0.1788 0.010 1.030 1.2 110.5 16.4 258 0.207 2_sol: 0.1130 0.1605 0.010 1.030 1.2 110.5 15.5 219 n/a 2_weight: 0.1130 0.1605 0.010 1.030 1.2 110.5 15.5 219 n/a 2_xyzrec: 0.1028 0.1741 0.009 0.948 1.2 110.5 15.5 219 n/a 2_adp: 0.0953 0.1782 0.009 0.948 0.0 107.6 16.5 219 n/a 2_regHadp: 0.0949 0.1784 0.009 0.948 0.0 107.6 16.5 219 n/a 2_occ: 0.0947 0.1777 0.009 0.948 0.0 107.6 16.5 219 n/a 3_bss: 0.0948 0.1776 0.009 0.948 0.0 107.6 16.5 219 n/a 3_settarget: 0.0948 0.1776 0.009 0.948 0.0 107.6 16.5 219 n/a 3_updatecdl: 0.0948 0.1776 0.009 0.954 0.0 107.6 16.5 219 n/a 3_nqh: 0.0950 0.1774 0.009 0.954 0.0 107.6 16.5 219 n/a 3_sol: 0.1044 0.1728 0.009 0.954 0.0 107.6 16.5 229 n/a 3_weight: 0.1044 0.1728 0.009 0.954 0.0 107.6 16.5 229 n/a 3_xyzrec: 0.0939 0.1827 0.011 1.066 0.0 107.6 16.5 229 n/a 3_adp: 0.0897 0.1845 0.011 1.066 0.0 107.2 16.7 229 n/a 3_regHadp: 0.0903 0.1855 0.011 1.066 0.0 107.2 16.7 229 n/a 3_occ: 0.0891 0.1844 0.011 1.066 0.0 107.2 16.7 229 n/a 4_bss: 0.0886 0.1845 0.011 1.066 0.0 107.2 16.6 229 n/a 4_settarget: 0.0886 0.1845 0.011 1.066 0.0 107.2 16.6 229 n/a 4_updatecdl: 0.0886 0.1845 0.011 1.077 0.0 107.2 16.6 229 n/a 4_nqh: 0.0886 0.1845 0.011 1.077 0.0 107.2 16.6 229 n/a 4_sol: 0.1005 0.1779 0.011 1.077 0.0 107.2 16.7 221 n/a 4_weight: 0.1005 0.1779 0.011 1.077 0.0 107.2 16.7 221 n/a 4_xyzrec: 0.0918 0.1858 0.011 1.062 0.0 107.2 16.7 221 n/a 4_adp: 0.0893 0.1864 0.011 1.062 0.0 105.3 16.8 221 n/a 4_regHadp: 0.0897 0.1869 0.011 1.062 0.0 105.3 16.8 221 n/a 4_occ: 0.0886 0.1859 0.011 1.062 0.0 105.3 16.8 221 n/a 5_bss: 0.0885 0.1858 0.011 1.062 0.0 105.3 16.8 221 n/a 5_settarget: 0.0885 0.1858 0.011 1.062 0.0 105.3 16.8 221 n/a 5_updatecdl: 0.0885 0.1858 0.011 1.057 0.0 105.3 16.8 221 n/a 5_setrh: 0.0888 0.1856 0.011 1.057 0.0 105.3 16.8 221 n/a 5_nqh: 0.0888 0.1856 0.011 1.057 0.0 105.3 16.8 221 n/a 5_sol: 0.0962 0.1848 0.011 1.057 0.0 105.3 16.9 225 n/a 5_weight: 0.0962 0.1848 0.011 1.057 0.0 105.3 16.9 225 n/a 5_xyzrec: 0.0914 0.1887 0.011 1.131 0.0 105.3 16.9 225 n/a 5_adp: 0.0896 0.1899 0.011 1.131 0.0 103.9 17.1 225 n/a 5_regHadp: 0.0900 0.1904 0.011 1.131 0.0 103.9 17.1 225 n/a 5_occ: 0.0891 0.1894 0.011 1.131 0.0 103.9 17.1 225 n/a end: 0.0891 0.1893 0.011 1.131 0.0 103.9 17.1 225 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2686906_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2686906_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9100 Refinement macro-cycles (run) : 479.3500 Write final files (write_after_run_outputs) : 10.8500 Total : 494.1100 Total CPU time: 8.58 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:56 PST -0800 (1735492736.48 s) Start R-work = 0.1575, R-free = 0.1580 Final R-work = 0.0891, R-free = 0.1893 =============================================================================== Job complete usr+sys time: 522.53 seconds wall clock time: 9 minutes 4.93 seconds (544.93 seconds total)