Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1446411.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1446411.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1446411.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" 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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.89, per 1000 atoms: 0.56 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 201.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.88: 324 0.88 - 1.14: 1275 1.14 - 1.40: 599 1.40 - 1.65: 899 1.65 - 1.91: 56 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.243 1.053 0.190 9.50e-03 1.11e+04 4.02e+02 bond pdb=" C SER A 161 " pdb=" N PHE A 162 " ideal model delta sigma weight residual 1.335 1.079 0.256 1.31e-02 5.83e+03 3.81e+02 bond pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.374 1.564 -0.190 1.10e-02 8.26e+03 2.98e+02 bond pdb=" CA THR A 125 " pdb=" C THR A 125 " ideal model delta sigma weight residual 1.523 1.736 -0.212 1.24e-02 6.50e+03 2.93e+02 bond pdb=" C ALA A 165 " pdb=" O ALA A 165 " ideal model delta sigma weight residual 1.237 1.043 0.193 1.17e-02 7.31e+03 2.73e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 2961 4.31 - 8.63: 1896 8.63 - 12.94: 732 12.94 - 17.26: 168 17.26 - 21.57: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OD1BASN A 76 " pdb=" CG BASN A 76 " pdb=" ND2BASN A 76 " ideal model delta sigma weight residual 122.60 136.71 -14.11 1.00e+00 1.00e+00 1.99e+02 angle pdb=" O SER A 3 " pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 123.03 107.17 15.86 1.13e+00 7.83e-01 1.97e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 106.99 12.21 9.00e-01 1.23e+00 1.84e+02 angle pdb=" C LYS A 89 " pdb=" N BGLU A 90 " pdb=" CA BGLU A 90 " ideal model delta sigma weight residual 120.54 138.79 -18.25 1.35e+00 5.49e-01 1.83e+02 angle pdb=" N LYS A 182 " pdb=" CA LYS A 182 " pdb=" C LYS A 182 " ideal model delta sigma weight residual 111.71 127.15 -15.44 1.15e+00 7.56e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 17.86: 1310 17.86 - 35.69: 119 35.69 - 53.52: 38 53.52 - 71.35: 11 71.35 - 89.19: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 88 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " pdb=" CB VAL A 88 " ideal model delta harmonic sigma weight residual -122.00 -145.27 23.27 0 2.50e+00 1.60e-01 8.67e+01 dihedral pdb=" N ALA A 39 " pdb=" C ALA A 39 " pdb=" CA ALA A 39 " pdb=" CB ALA A 39 " ideal model delta harmonic sigma weight residual 122.90 103.92 18.98 0 2.50e+00 1.60e-01 5.76e+01 dihedral pdb=" N BGLU A 90 " pdb=" C BGLU A 90 " pdb=" CA BGLU A 90 " pdb=" CB BGLU A 90 " ideal model delta harmonic sigma weight residual 122.80 140.95 -18.15 0 2.50e+00 1.60e-01 5.27e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.248: 110 0.248 - 0.496: 85 0.496 - 0.743: 36 0.743 - 0.991: 10 0.991 - 1.238: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.39 -1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.57 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA ASP A 131 " pdb=" N ASP A 131 " pdb=" C ASP A 131 " pdb=" CB ASP A 131 " both_signs ideal model delta sigma weight residual False 2.51 1.54 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=" CD ARG A 145 " -0.170 9.50e-02 1.11e+02 9.09e-02 1.17e+02 pdb=" NE ARG A 145 " -0.068 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.089 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.111 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.021 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.126 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " -0.065 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.008 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.057 2.00e-02 2.50e+03 6.23e-02 1.17e+02 pdb=" CG PHE A 164 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.094 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.130 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.024 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.022 2.00e-02 2.50e+03 5.69e-02 9.72e+01 pdb=" CG PHE A 119 " -0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.061 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1266 2.35 - 2.92: 8275 2.92 - 3.48: 10535 3.48 - 4.04: 15103 4.04 - 4.60: 21473 Nonbonded interactions: 56652 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.792 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.830 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.836 2.100 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.847 2.270 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.870 2.450 x-y,-y,-z-4/3 ... (remaining 56647 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_1446411_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= 0.3614 r_free= 0.1943 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.459608 | | target function (ml) not normalized (work): 21985.865410 | | target function (ml) not normalized (free): 1141.171191 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3810 0.2156 4.8417 4.8769| | 2: 3.78 - 3.00 1.00 2430 110 0.3375 0.1583 4.0665 4.0786| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.68 0.83 0.13 6586.62| | 2: 3.78 - 3.00 2430 110 0.94 11.25 1.48 0.26 446.97| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 386.81 max = 12066.95 mean = 3560.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.23| |phase err.(test): min = 0.00 max = 89.95 mean = 33.15| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.261 1557 Z= 5.495 Angle : 5.249 18.248 2118 Z= 3.703 Chirality : 0.391 1.238 243 Planarity : 0.030 0.076 284 Dihedral : 14.342 89.186 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.89 % Cbeta Deviations : 23.24 % 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: -2.68 (0.46), residues: 224 helix: -2.53 (0.35), residues: 109 sheet: -1.11 (0.93), residues: 28 loop : -0.59 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.121 0.035 ARG A 156 TYR 0.032 0.017 TYR A 141 PHE 0.088 0.033 PHE A 119 HIS 0.083 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= 0.3614 r_free= 0.1943 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.459608 | | target function (ml) not normalized (work): 21985.865410 | | target function (ml) not normalized (free): 1141.171191 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3566 0.3646 0.2027 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3566 0.3646 0.2027 n_refl.: 5182 remove outliers: r(all,work,free)=0.2508 0.2536 0.2027 n_refl.: 5178 overall B=-1.15 to atoms: r(all,work,free)=0.2462 0.2489 0.2009 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1558 0.1560 0.1529 n_refl.: 5178 remove outliers: r(all,work,free)=0.1554 0.1555 0.1529 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 0.3932 449.958 405.508 0.618 1.092 0.393 11.894-9.307 99.02 97 4 0.1889 714.794 694.830 0.887 1.085 0.381 9.237-7.194 100.00 213 7 0.2193 584.560 575.159 0.919 1.075 0.351 7.162-5.571 100.00 427 22 0.2320 438.641 423.021 0.894 1.059 0.290 5.546-4.326 100.00 867 58 0.1373 602.192 594.610 0.952 1.032 0.253 4.315-3.360 100.00 1859 96 0.1298 572.691 567.070 1.043 0.987 0.163 3.356-3.002 100.00 1373 60 0.1603 441.111 433.811 1.078 0.942 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-5.1257 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1529 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=0.1555 r_free=0.1533 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.704386 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.838005 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 0.1160 0.1817 0.0657 0.010 1.0 3.5 0.5 0.0 0 9.352 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 18.17 6.57 3.013 17.711 1.838 0.018 10.24 18.13 7.90 4.866 17.830 1.838 0.015 Individual atomic B min max mean iso aniso Overall: 3.21 113.15 18.96 5.30 1785 0 Protein: 3.21 113.04 16.24 5.29 1519 0 Water: 5.72 113.15 34.80 N/A 258 0 Other: 17.80 39.07 25.30 N/A 8 0 Chain A: 3.21 113.15 18.96 N/A 1785 0 Histogram: Values Number of atoms 3.21 - 14.21 884 14.21 - 25.20 503 25.20 - 36.19 196 36.19 - 47.19 109 47.19 - 58.18 60 58.18 - 69.18 16 69.18 - 80.17 8 80.17 - 91.16 5 91.16 - 102.16 1 102.16 - 113.15 3 =========================== Idealize ADP of riding H ========================== r_work=0.1024 r_free=0.1813 r_work=0.1018 r_free=0.1818 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1018 r_free = 0.1818 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 = 0.1014 r_free = 0.1819 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.13 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= 0.1014 r_free= 0.1819 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013971 | | target function (ls_wunit_k1) not normalized (work): 68.791528 | | target function (ls_wunit_k1) not normalized (free): 10.740795 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1055 0.1014 0.1819 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2148 0.2148 0.2250 n_refl.: 5176 remove outliers: r(all,work,free)=0.2148 0.2148 0.2250 n_refl.: 5176 overall B=-1.06 to atoms: r(all,work,free)=0.2100 0.2099 0.2236 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1062 0.1021 0.1820 n_refl.: 5176 remove outliers: r(all,work,free)=0.1062 0.1021 0.1820 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 0.3301 316.724 311.646 0.675 1.001 0.376 11.894-9.307 99.02 97 4 0.1534 503.141 495.003 0.955 1.003 0.351 9.237-7.194 100.00 213 7 0.1697 411.470 412.666 0.991 1.003 0.305 7.162-5.571 100.00 427 22 0.1619 308.758 305.335 0.954 1.002 0.282 5.546-4.326 100.00 867 58 0.0915 423.881 419.711 0.971 1.001 0.212 4.315-3.360 100.00 1859 96 0.0776 403.115 403.082 1.025 0.999 0.163 3.356-3.002 100.00 1373 60 0.1010 310.496 308.907 1.004 0.997 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.7761 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1021 r_free=0.1820 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1021 r_free=0.1820 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1021 r_free=0.1820 | n_water=258 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1050 r_free=0.1823 | n_water=247 | time (s): 21.100 (total time: 21.810) Filter (q & B) r_work=0.1051 r_free=0.1830 | n_water=245 | time (s): 1.760 (total time: 23.570) Compute maps r_work=0.1051 r_free=0.1830 | n_water=245 | time (s): 0.660 (total time: 24.230) Filter (map) r_work=0.1374 r_free=0.1863 | n_water=140 | time (s): 1.800 (total time: 26.030) Find peaks r_work=0.1374 r_free=0.1863 | n_water=140 | time (s): 0.610 (total time: 26.640) Add new water r_work=0.1746 r_free=0.2166 | n_water=239 | time (s): 1.480 (total time: 28.120) Refine new water occ: r_work=0.1193 r_free=0.1736 adp: r_work=0.1159 r_free=0.1731 occ: r_work=0.1156 r_free=0.1700 adp: r_work=0.1156 r_free=0.1700 occ: r_work=0.1156 r_free=0.1700 adp: r_work=0.1156 r_free=0.1700 ADP+occupancy (water only), MIN, final r_work=0.1156 r_free=0.1700 r_work=0.1156 r_free=0.1700 | n_water=239 | time (s): 8.960 (total time: 37.080) Filter (q & B) r_work=0.1156 r_free=0.1700 | n_water=239 | time (s): 0.780 (total time: 37.860) Filter (dist only) r_work=0.1158 r_free=0.1698 | n_water=237 | time (s): 17.680 (total time: 55.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.302554 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.630697 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 0.1016 0.1768 0.0752 0.009 0.9 4.5 0.5 0.6 0 10.651 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.16 17.68 7.52 4.776 18.173 2.631 0.014 9.46 17.87 8.41 5.542 18.484 2.631 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 111.17 17.47 6.45 1764 0 Protein: 1.39 111.17 16.14 6.43 1519 0 Water: 0.00 65.34 25.71 N/A 237 0 Other: 11.74 42.99 26.59 N/A 8 0 Chain A: 1.39 111.17 16.89 N/A 1665 0 Chain S: 0.00 48.42 27.20 N/A 99 0 Histogram: Values Number of atoms 0.00 - 11.12 605 11.12 - 22.23 738 22.23 - 33.35 238 33.35 - 44.47 115 44.47 - 55.58 36 55.58 - 66.70 21 66.70 - 77.82 4 77.82 - 88.94 3 88.94 - 100.05 2 100.05 - 111.17 2 =========================== Idealize ADP of riding H ========================== r_work=0.0946 r_free=0.1787 r_work=0.0943 r_free=0.1786 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0943 r_free = 0.1786 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 = 0.0941 r_free = 0.1790 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.27 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= 0.0941 r_free= 0.1790 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011989 | | target function (ls_wunit_k1) not normalized (work): 59.035747 | | target function (ls_wunit_k1) not normalized (free): 9.912179 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0984 0.0941 0.1790 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2168 0.2166 0.2315 n_refl.: 5176 remove outliers: r(all,work,free)=0.2168 0.2166 0.2315 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2168 0.2166 0.2315 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0981 0.0938 0.1783 n_refl.: 5176 remove outliers: r(all,work,free)=0.0980 0.0937 0.1783 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3185 314.056 302.760 0.652 1.006 0.365 11.894-9.307 99.02 97 4 0.1448 503.141 498.728 0.943 1.007 0.331 9.237-7.194 100.00 213 7 0.1440 411.470 412.615 0.987 1.007 0.306 7.162-5.571 100.00 427 22 0.1418 308.758 306.319 0.961 1.006 0.290 5.546-4.326 100.00 867 58 0.0785 423.881 421.645 0.977 1.003 0.240 4.315-3.360 100.00 1859 96 0.0730 403.115 402.549 1.033 0.998 0.190 3.356-3.002 100.00 1373 60 0.0973 310.496 309.643 1.017 0.993 0.100 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-5.1502 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0937 r_free=0.1783 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0937 r_free=0.1782 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0937 r_free=0.1782 | n_water=237 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0962 r_free=0.1795 | n_water=231 | time (s): 19.630 (total time: 20.290) Filter (q & B) r_work=0.0970 r_free=0.1791 | n_water=230 | time (s): 1.660 (total time: 21.950) Compute maps r_work=0.0970 r_free=0.1791 | n_water=230 | time (s): 0.520 (total time: 22.470) Filter (map) r_work=0.1285 r_free=0.1886 | n_water=148 | time (s): 1.310 (total time: 23.780) Find peaks r_work=0.1285 r_free=0.1886 | n_water=148 | time (s): 0.400 (total time: 24.180) Add new water r_work=0.1655 r_free=0.2180 | n_water=230 | time (s): 1.480 (total time: 25.660) Refine new water occ: r_work=0.1075 r_free=0.1750 adp: r_work=0.1074 r_free=0.1757 occ: r_work=0.1064 r_free=0.1739 adp: r_work=0.1063 r_free=0.1747 occ: r_work=0.1055 r_free=0.1728 adp: r_work=0.1055 r_free=0.1728 ADP+occupancy (water only), MIN, final r_work=0.1055 r_free=0.1728 r_work=0.1055 r_free=0.1728 | n_water=230 | time (s): 9.910 (total time: 35.570) Filter (q & B) r_work=0.1055 r_free=0.1728 | n_water=230 | time (s): 1.060 (total time: 36.630) Filter (dist only) r_work=0.1075 r_free=0.1732 | n_water=228 | time (s): 20.090 (total time: 56.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.100734 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.221814 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 0.0948 0.1837 0.0890 0.010 1.0 4.2 0.5 0.6 0 0.550 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.48 18.37 8.90 5.469 18.891 0.222 5.137 9.01 18.78 9.77 7.293 18.899 0.222 5.039 Individual atomic B min max mean iso aniso Overall: 0.00 111.02 17.28 8.90 1755 0 Protein: 0.00 111.02 16.22 8.88 1519 0 Water: 0.00 60.34 23.94 N/A 228 0 Other: 12.96 49.11 28.71 N/A 8 0 Chain A: 0.00 111.02 16.85 N/A 1649 0 Chain S: 0.00 55.01 23.99 N/A 106 0 Histogram: Values Number of atoms 0.00 - 11.10 601 11.10 - 22.20 728 22.20 - 33.31 244 33.31 - 44.41 116 44.41 - 55.51 34 55.51 - 66.61 16 66.61 - 77.72 10 77.72 - 88.82 1 88.82 - 99.92 4 99.92 - 111.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1878 r_work=0.0905 r_free=0.1891 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0905 r_free = 0.1891 target_work(ml) = 5.042 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0897 r_free = 0.1883 target_work(ml) = 5.037 | | occupancies: max = 1.00 min = 0.27 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= 0.0897 r_free= 0.1883 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.036678 | | target function (ml) not normalized (work): 24795.566511 | | target function (ml) not normalized (free): 1852.539147 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0947 0.0897 0.1883 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2170 0.2173 0.2257 n_refl.: 5175 remove outliers: r(all,work,free)=0.2170 0.2173 0.2257 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2170 0.2173 0.2257 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0941 0.0892 0.1878 n_refl.: 5175 remove outliers: r(all,work,free)=0.0939 0.0890 0.1878 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 0.3739 316.145 284.701 0.604 0.993 0.345 11.894-9.307 99.02 97 4 0.1811 503.141 488.471 0.961 0.997 0.342 9.237-7.194 100.00 213 7 0.1771 411.470 405.771 1.010 0.998 0.300 7.162-5.571 100.00 427 22 0.1779 308.758 300.689 0.987 0.999 0.300 5.546-4.326 100.00 867 58 0.0901 423.881 419.159 1.009 1.000 0.250 4.315-3.360 100.00 1859 96 0.0609 403.115 402.359 1.073 1.002 0.200 3.356-3.002 100.00 1373 60 0.0631 310.496 310.484 1.060 1.003 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.3331 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0890 r_free=0.1878 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.0890 r_free=0.1876 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0890 r_free=0.1876 | n_water=228 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0897 r_free=0.1895 | n_water=226 | time (s): 18.590 (total time: 19.250) Filter (q & B) r_work=0.0942 r_free=0.1911 | n_water=224 | time (s): 1.490 (total time: 20.740) Compute maps r_work=0.0942 r_free=0.1911 | n_water=224 | time (s): 0.560 (total time: 21.300) Filter (map) r_work=0.1231 r_free=0.1977 | n_water=156 | time (s): 1.590 (total time: 22.890) Find peaks r_work=0.1231 r_free=0.1977 | n_water=156 | time (s): 0.390 (total time: 23.280) Add new water r_work=0.1575 r_free=0.2195 | n_water=238 | time (s): 1.290 (total time: 24.570) Refine new water occ: r_work=0.1018 r_free=0.1817 adp: r_work=0.1014 r_free=0.1832 occ: r_work=0.1006 r_free=0.1813 adp: r_work=0.1005 r_free=0.1825 occ: r_work=0.0997 r_free=0.1806 adp: r_work=0.0997 r_free=0.1817 ADP+occupancy (water only), MIN, final r_work=0.0997 r_free=0.1817 r_work=0.0997 r_free=0.1817 | n_water=238 | time (s): 12.080 (total time: 36.650) Filter (q & B) r_work=0.0996 r_free=0.1822 | n_water=236 | time (s): 1.580 (total time: 38.230) Filter (dist only) r_work=0.0996 r_free=0.1826 | n_water=235 | time (s): 18.200 (total time: 56.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.995984 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.187478 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 0.0901 0.1899 0.0998 0.010 1.0 4.8 0.5 0.6 0 0.498 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.01 18.99 9.98 6.998 19.054 0.187 4.985 8.77 19.29 10.52 8.156 19.166 0.187 4.915 Individual atomic B min max mean iso aniso Overall: 0.00 111.06 17.64 10.57 1762 0 Protein: 0.00 111.06 16.62 10.56 1519 0 Water: 0.00 59.97 23.81 N/A 235 0 Other: 12.21 51.14 28.53 N/A 8 0 Chain A: 0.00 111.06 17.09 N/A 1636 0 Chain S: 0.00 59.97 24.74 N/A 126 0 Histogram: Values Number of atoms 0.00 - 11.11 603 11.11 - 22.21 706 22.21 - 33.32 263 33.32 - 44.42 117 44.42 - 55.53 40 55.53 - 66.64 15 66.64 - 77.74 10 77.74 - 88.85 3 88.85 - 99.95 4 99.95 - 111.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.0877 r_free=0.1929 r_work=0.0882 r_free=0.1936 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0882 r_free = 0.1936 target_work(ml) = 4.920 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0869 r_free = 0.1913 target_work(ml) = 4.911 | | occupancies: max = 1.00 min = 0.27 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= 0.0869 r_free= 0.1913 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.910897 | | target function (ml) not normalized (work): 24171.436194 | | target function (ml) not normalized (free): 2236.245268 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0922 0.0869 0.1913 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2122 0.2119 0.2266 n_refl.: 5174 remove outliers: r(all,work,free)=0.2122 0.2119 0.2266 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2122 0.2119 0.2266 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0918 0.0866 0.1903 n_refl.: 5174 remove outliers: r(all,work,free)=0.0918 0.0866 0.1903 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 0.3836 316.145 287.672 0.605 0.988 0.314 11.894-9.307 99.02 97 4 0.1959 503.141 486.822 0.992 0.993 0.310 9.237-7.194 100.00 213 7 0.2089 411.470 402.657 1.062 0.996 0.275 7.162-5.571 100.00 427 22 0.2018 308.758 298.825 1.039 0.997 0.270 5.546-4.326 100.00 867 58 0.0960 423.881 418.080 1.069 0.999 0.240 4.315-3.360 100.00 1859 96 0.0542 403.115 402.777 1.143 1.002 0.210 3.356-3.002 100.00 1373 60 0.0435 310.496 310.393 1.132 1.005 0.084 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.5193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0866 r_free=0.1903 After: r_work=0.0869 r_free=0.1902 ================================== NQH flips ================================== r_work=0.0869 r_free=0.1902 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0869 r_free=0.1902 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0869 r_free=0.1902 | n_water=235 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.0888 r_free=0.1913 | n_water=231 | time (s): 17.950 (total time: 18.450) Filter (q & B) r_work=0.1005 r_free=0.1908 | n_water=228 | time (s): 1.370 (total time: 19.820) Compute maps r_work=0.1005 r_free=0.1908 | n_water=228 | time (s): 0.520 (total time: 20.340) Filter (map) r_work=0.1253 r_free=0.1991 | n_water=163 | time (s): 1.730 (total time: 22.070) Find peaks r_work=0.1253 r_free=0.1991 | n_water=163 | time (s): 0.590 (total time: 22.660) Add new water r_work=0.1521 r_free=0.2209 | n_water=229 | time (s): 1.910 (total time: 24.570) Refine new water occ: r_work=0.1002 r_free=0.1896 adp: r_work=0.0991 r_free=0.1910 occ: r_work=0.0984 r_free=0.1900 adp: r_work=0.0983 r_free=0.1904 occ: r_work=0.0978 r_free=0.1894 adp: r_work=0.0977 r_free=0.1898 ADP+occupancy (water only), MIN, final r_work=0.0977 r_free=0.1898 r_work=0.0977 r_free=0.1898 | n_water=229 | time (s): 14.690 (total time: 39.260) Filter (q & B) r_work=0.0978 r_free=0.1896 | n_water=228 | time (s): 1.300 (total time: 40.560) Filter (dist only) r_work=0.0988 r_free=0.1889 | n_water=225 | time (s): 17.200 (total time: 57.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.942635 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.193494 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 0.0916 0.1890 0.0974 0.010 1.1 7.4 0.5 0.6 0 0.471 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.16 18.90 9.74 8.104 19.440 0.193 4.979 8.94 18.98 10.04 9.020 19.529 0.193 4.917 Individual atomic B min max mean iso aniso Overall: 0.00 112.05 17.86 11.83 1752 0 Protein: 0.00 112.05 16.95 11.82 1519 0 Water: 0.00 67.85 23.70 N/A 225 0 Other: 12.79 50.79 28.26 N/A 8 0 Chain A: 0.00 112.05 17.38 N/A 1631 0 Chain S: 0.00 67.85 24.36 N/A 121 0 Histogram: Values Number of atoms 0.00 - 11.20 604 11.20 - 22.41 693 22.41 - 33.61 270 33.61 - 44.82 102 44.82 - 56.02 49 56.02 - 67.23 14 67.23 - 78.43 10 78.43 - 89.64 4 89.64 - 100.84 5 100.84 - 112.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.0894 r_free=0.1898 r_work=0.0897 r_free=0.1900 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1900 target_work(ml) = 4.921 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0889 r_free = 0.1897 target_work(ml) = 4.915 | | 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= 0.0889 r_free= 0.1897 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.915218 | | target function (ml) not normalized (work): 24192.704521 | | target function (ml) not normalized (free): 2251.745359 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1271 0.1918 5.5037 6.2259| | 2: 3.78 - 3.00 1.00 2430 110 0.0424 0.1860 4.3117 12.433| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.91 12.34 1.00 0.90 12617.20| | 2: 3.78 - 3.00 2430 110 0.99 1.80 1.00 0.92 821.84| |alpha: min = 0.89 max = 0.92 mean = 0.91| |beta: min = 520.04 max = 21191.66 mean = 6793.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.88 mean = 7.14| |phase err.(test): min = 0.00 max = 89.01 mean = 7.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0940 0.0889 0.1897 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2181 0.2183 0.2267 n_refl.: 5174 remove outliers: r(all,work,free)=0.2181 0.2183 0.2267 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2181 0.2183 0.2267 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0939 0.0888 0.1901 n_refl.: 5174 remove outliers: r(all,work,free)=0.0939 0.0888 0.1901 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 0.3791 316.145 287.488 0.639 0.988 0.340 11.894-9.307 99.02 97 4 0.1952 503.141 488.103 1.005 0.994 0.340 9.237-7.194 100.00 213 7 0.2194 411.470 401.163 1.055 0.997 0.293 7.162-5.571 100.00 427 22 0.2074 308.758 299.843 1.033 0.998 0.277 5.546-4.326 100.00 867 58 0.1021 423.881 417.551 1.069 1.000 0.240 4.315-3.360 100.00 1859 96 0.0566 403.115 403.003 1.156 1.002 0.209 3.356-3.002 100.00 1373 60 0.0399 310.496 310.563 1.150 1.004 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-9.0440 ================= 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 : 0.3614 0.1943 0.082 5.249 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1529 0.082 5.249 7.7 118.2 18.7 258 0.000 1_settarget: 0.1555 0.1529 0.082 5.249 7.7 118.2 18.7 258 0.000 1_nqh: 0.1555 0.1533 0.082 5.249 7.7 118.2 18.7 258 0.003 1_weight: 0.1555 0.1533 0.082 5.249 7.7 118.2 18.7 258 0.003 1_xyzrec: 0.1160 0.1817 0.010 0.967 7.7 118.2 18.7 258 0.220 1_adp: 0.1024 0.1813 0.010 0.967 3.2 113.2 19.0 258 0.220 1_regHadp: 0.1018 0.1818 0.010 0.967 3.2 113.2 19.0 258 0.220 1_occ: 0.1014 0.1819 0.010 0.967 3.2 113.2 19.0 258 0.220 2_bss: 0.1021 0.1820 0.010 0.967 2.1 112.1 17.9 258 0.220 2_settarget: 0.1021 0.1820 0.010 0.967 2.1 112.1 17.9 258 0.220 2_updatecdl: 0.1021 0.1820 0.010 1.001 2.1 112.1 17.9 258 0.220 2_nqh: 0.1021 0.1820 0.010 1.001 2.1 112.1 17.9 258 0.220 2_sol: 0.1158 0.1698 0.010 1.001 1.6 112.0 16.9 237 n/a 2_weight: 0.1158 0.1698 0.010 1.001 1.6 112.0 16.9 237 n/a 2_xyzrec: 0.1016 0.1768 0.009 0.943 1.6 112.0 16.9 237 n/a 2_adp: 0.0946 0.1787 0.009 0.943 0.0 111.2 17.5 237 n/a 2_regHadp: 0.0943 0.1786 0.009 0.943 0.0 111.2 17.5 237 n/a 2_occ: 0.0941 0.1790 0.009 0.943 0.0 111.2 17.5 237 n/a 3_bss: 0.0937 0.1783 0.009 0.943 0.0 111.2 17.5 237 n/a 3_settarget: 0.0937 0.1783 0.009 0.943 0.0 111.2 17.5 237 n/a 3_updatecdl: 0.0937 0.1783 0.009 0.948 0.0 111.2 17.5 237 n/a 3_nqh: 0.0937 0.1782 0.009 0.948 0.0 111.2 17.5 237 n/a 3_sol: 0.1075 0.1732 0.009 0.948 1.4 111.2 17.3 228 n/a 3_weight: 0.1075 0.1732 0.009 0.948 1.4 111.2 17.3 228 n/a 3_xyzrec: 0.0948 0.1837 0.010 1.019 1.4 111.2 17.3 228 n/a 3_adp: 0.0901 0.1878 0.010 1.019 0.0 111.0 17.3 228 n/a 3_regHadp: 0.0905 0.1891 0.010 1.019 0.0 111.0 17.3 228 n/a 3_occ: 0.0897 0.1883 0.010 1.019 0.0 111.0 17.3 228 n/a 4_bss: 0.0890 0.1878 0.010 1.019 0.0 111.0 17.3 228 n/a 4_settarget: 0.0890 0.1878 0.010 1.019 0.0 111.0 17.3 228 n/a 4_updatecdl: 0.0890 0.1878 0.010 1.026 0.0 111.0 17.3 228 n/a 4_nqh: 0.0890 0.1876 0.010 1.026 0.0 111.0 17.3 228 n/a 4_sol: 0.0996 0.1826 0.010 1.026 0.0 111.0 17.4 235 n/a 4_weight: 0.0996 0.1826 0.010 1.026 0.0 111.0 17.4 235 n/a 4_xyzrec: 0.0901 0.1899 0.010 1.012 0.0 111.0 17.4 235 n/a 4_adp: 0.0877 0.1929 0.010 1.012 0.0 111.1 17.6 235 n/a 4_regHadp: 0.0882 0.1936 0.010 1.012 0.0 111.1 17.6 235 n/a 4_occ: 0.0869 0.1913 0.010 1.012 0.0 111.1 17.6 235 n/a 5_bss: 0.0866 0.1903 0.010 1.012 0.0 111.1 17.6 235 n/a 5_settarget: 0.0866 0.1903 0.010 1.012 0.0 111.1 17.6 235 n/a 5_updatecdl: 0.0866 0.1903 0.010 1.021 0.0 111.1 17.6 235 n/a 5_setrh: 0.0869 0.1902 0.010 1.021 0.0 111.1 17.6 235 n/a 5_nqh: 0.0869 0.1902 0.010 1.021 0.0 111.1 17.6 235 n/a 5_sol: 0.0988 0.1889 0.010 1.021 0.0 111.1 17.7 225 n/a 5_weight: 0.0988 0.1889 0.010 1.021 0.0 111.1 17.7 225 n/a 5_xyzrec: 0.0916 0.1890 0.010 1.083 0.0 111.1 17.7 225 n/a 5_adp: 0.0894 0.1898 0.010 1.083 0.0 112.0 17.9 225 n/a 5_regHadp: 0.0897 0.1900 0.010 1.083 0.0 112.0 17.9 225 n/a 5_occ: 0.0889 0.1897 0.010 1.083 0.0 112.0 17.9 225 n/a end: 0.0888 0.1901 0.010 1.083 0.0 112.0 17.9 225 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1446411_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1446411_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6200 Refinement macro-cycles (run) : 498.5500 Write final files (write_after_run_outputs) : 9.6500 Total : 511.8200 Total CPU time: 8.92 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:16 PST -0800 (1735492756.43 s) Start R-work = 0.1555, R-free = 0.1529 Final R-work = 0.0888, R-free = 0.1901 =============================================================================== Job complete usr+sys time: 541.96 seconds wall clock time: 9 minutes 23.61 seconds (563.61 seconds total)