Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8736282.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=2 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 = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8736282.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8736282.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 1 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: 1.57, per 1000 atoms: 0.46 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: 0.29 Conformation dependent library (CDL) restraints added in 126.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.61 - 0.87: 288 0.87 - 1.13: 1291 1.13 - 1.39: 588 1.39 - 1.65: 919 1.65 - 1.91: 67 Bond restraints: 3153 Sorted by residual: bond pdb=" CA PRO A 73 " pdb=" C PRO A 73 " ideal model delta sigma weight residual 1.521 1.318 0.203 1.20e-02 6.94e+03 2.87e+02 bond pdb=" C LEU A 185 " pdb=" O LEU A 185 " ideal model delta sigma weight residual 1.236 1.013 0.223 1.32e-02 5.74e+03 2.85e+02 bond pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " ideal model delta sigma weight residual 1.522 1.322 0.200 1.19e-02 7.06e+03 2.83e+02 bond pdb=" C VAL A 51 " pdb=" O VAL A 51 " ideal model delta sigma weight residual 1.237 1.417 -0.180 1.08e-02 8.57e+03 2.77e+02 bond pdb=" CA ILE A 31 " pdb=" C ILE A 31 " ideal model delta sigma weight residual 1.523 1.333 0.190 1.14e-02 7.69e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 3452 5.28 - 10.55: 1819 10.55 - 15.82: 448 15.82 - 21.09: 54 21.09 - 26.37: 4 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.35 108.99 14.36 9.50e-01 1.11e+00 2.28e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.57 135.23 -12.66 9.20e-01 1.18e+00 1.89e+02 angle pdb=" O GLY A 136 " pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 122.42 105.72 16.70 1.31e+00 5.83e-01 1.62e+02 angle pdb=" OE1 GLN A 95 " pdb=" CD GLN A 95 " pdb=" NE2 GLN A 95 " ideal model delta sigma weight residual 122.60 109.95 12.65 1.00e+00 1.00e+00 1.60e+02 angle pdb=" O VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " ideal model delta sigma weight residual 122.62 108.76 13.86 1.17e+00 7.31e-01 1.40e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.87: 1327 17.87 - 35.74: 100 35.74 - 53.61: 38 53.61 - 71.48: 15 71.48 - 89.35: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N VAL A 23 " pdb=" C VAL A 23 " pdb=" CA VAL A 23 " pdb=" CB VAL A 23 " ideal model delta harmonic sigma weight residual 123.40 104.71 18.69 0 2.50e+00 1.60e-01 5.59e+01 dihedral pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CA PHE A 119 " pdb=" CB PHE A 119 " ideal model delta harmonic sigma weight residual 122.80 140.50 -17.70 0 2.50e+00 1.60e-01 5.01e+01 dihedral pdb=" C BASN A 97 " pdb=" N BASN A 97 " pdb=" CA BASN A 97 " pdb=" CB BASN A 97 " ideal model delta harmonic sigma weight residual -122.60 -139.37 16.77 0 2.50e+00 1.60e-01 4.50e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.200: 92 0.200 - 0.397: 73 0.397 - 0.593: 41 0.593 - 0.789: 29 0.789 - 0.986: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PHE A 119 " pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CB PHE A 119 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CA VAL A 23 " pdb=" N VAL A 23 " pdb=" C VAL A 23 " pdb=" CB VAL A 23 " both_signs ideal model delta sigma weight residual False 2.44 3.36 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 3.39 -0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.077 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG ATYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.101 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.008 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.061 9.50e-02 1.11e+02 6.84e-02 9.63e+01 pdb=" NE ARG A 145 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.077 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " -0.067 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.099 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.023 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.086 2.00e-02 2.50e+03 5.52e-02 9.13e+01 pdb=" CG PHE A 164 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.077 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1060 2.32 - 2.89: 8105 2.89 - 3.46: 10509 3.46 - 4.03: 15335 4.03 - 4.60: 21607 Nonbonded interactions: 56616 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.754 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.778 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.813 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.834 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.834 2.450 ... (remaining 56611 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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_8736282_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2787 r_free= 0.1869 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.402923 | | target function (ml) not normalized (work): 71516.673818 | | target function (ml) not normalized (free): 3277.661261 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3180 0.2168 7.5008 5.028| | 2: 3.63 - 2.88 1.00 2711 122 0.2623 0.1787 4.3261 4.3525| | 3: 2.88 - 2.52 1.00 2682 148 0.2578 0.1796 4.1893 4.1966| | 4: 2.52 - 2.29 1.00 2661 139 0.2555 0.1574 3.5097 3.5651| | 5: 2.29 - 2.13 1.00 2678 122 0.2662 0.1527 3.4067 3.4711| | 6: 2.13 - 2.00 1.00 2692 117 0.2771 0.1927 3.3231 3.4793| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.72 0.77 0.23 1325.99| | 2: 3.63 - 2.88 2711 122 0.83 23.90 1.31 0.23 1325.99| | 3: 2.88 - 2.52 2682 148 0.73 33.19 1.29 0.23 1325.99| | 4: 2.52 - 2.29 2661 139 0.93 11.64 1.30 0.26 141.13| | 5: 2.29 - 2.13 2678 122 0.92 13.96 1.32 0.26 141.13| | 6: 2.13 - 2.00 2692 117 0.90 16.69 1.34 0.26 141.13| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 141.13 max = 1325.99 mean = 740.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 19.52| |phase err.(test): min = 0.00 max = 88.99 mean = 19.56| |-----------------------------------------------------------------------------| ----------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 0.238 1557 Z= 5.499 Angle : 5.270 16.705 2118 Z= 3.642 Chirality : 0.390 0.986 243 Planarity : 0.033 0.085 284 Dihedral : 13.762 89.347 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 35.68 % 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: -3.01 (0.46), residues: 224 helix: -3.33 (0.31), residues: 103 sheet: -0.11 (0.89), residues: 28 loop : -0.66 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.023 ARG A 145 TYR 0.087 0.040 TYR A 141 PHE 0.109 0.040 PHE A 164 HIS 0.107 0.036 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2787 r_free= 0.1869 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.402923 | | target function (ml) not normalized (work): 71516.673818 | | target function (ml) not normalized (free): 3277.661261 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2957 percent. r_work = 0.2916 r_free = 0.2011 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2864 0.2916 0.2011 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2864 0.2916 0.2011 n_refl.: 17050 remove outliers: r(all,work,free)=0.2156 0.2166 0.2011 n_refl.: 17045 overall B=-0.43 to atoms: r(all,work,free)=0.2127 0.2136 0.1992 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1612 0.1608 0.1682 n_refl.: 17045 remove outliers: r(all,work,free)=0.1611 0.1607 0.1682 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4082 395.041 362.492 0.659 1.011 0.403 11.894-9.307 99.02 97 4 0.1859 634.053 615.107 0.934 1.012 0.390 9.237-7.194 100.00 213 7 0.2160 518.591 510.592 0.962 1.012 0.354 7.162-5.571 100.00 427 22 0.2325 389.203 375.054 0.922 1.011 0.284 5.546-4.326 100.00 867 58 0.1404 534.314 528.401 0.961 1.009 0.220 4.315-3.360 100.00 1859 96 0.1303 508.138 503.699 1.019 1.006 0.191 3.356-2.611 100.00 3867 181 0.1633 333.817 329.418 1.013 1.000 0.101 2.608-2.000 99.99 8818 434 0.1640 217.592 213.702 1.033 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.5259 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1607 r_free=0.1682 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1609 r_free=0.1687 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.605292 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.894134 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1354 0.1636 0.0282 0.009 1.0 1.6 0.5 0.0 0 11.303 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.54 16.36 2.82 3.013 18.432 0.894 0.023 12.77 16.60 3.83 3.652 18.742 0.894 0.020 Individual atomic B min max mean iso aniso Overall: 6.23 113.87 20.05 4.08 1785 0 Protein: 6.23 112.40 17.29 4.08 1519 0 Water: 9.01 113.87 36.08 N/A 258 0 Other: 21.74 37.51 26.54 N/A 8 0 Chain A: 6.23 113.87 20.05 N/A 1785 0 Histogram: Values Number of atoms 6.23 - 16.99 1087 16.99 - 27.76 341 27.76 - 38.52 182 38.52 - 49.29 101 49.29 - 60.05 46 60.05 - 70.81 14 70.81 - 81.58 6 81.58 - 92.34 4 92.34 - 103.11 1 103.11 - 113.87 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1660 r_work=0.1280 r_free=0.1666 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1666 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1274 r_free = 0.1663 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1274 r_free= 0.1663 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019902 | | target function (ls_wunit_k1) not normalized (work): 323.146648 | | target function (ls_wunit_k1) not normalized (free): 27.308693 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1274 0.1663 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1919 0.1918 0.1999 n_refl.: 17044 remove outliers: r(all,work,free)=0.1919 0.1918 0.1999 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1890 0.1888 0.1982 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1652 n_refl.: 17044 remove outliers: r(all,work,free)=0.1291 0.1273 0.1652 n_refl.: 17042 ======================== 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 0.3608 303.130 280.841 0.625 1.000 0.368 11.894-9.307 99.02 97 4 0.1718 487.537 478.481 0.929 0.999 0.367 9.237-7.194 100.00 213 7 0.1833 398.756 396.488 0.971 0.998 0.341 7.162-5.571 100.00 427 22 0.1807 299.267 295.055 0.944 0.997 0.301 5.546-4.326 100.00 867 58 0.1029 410.846 409.392 0.970 0.995 0.211 4.315-3.360 100.00 1859 96 0.0922 390.718 390.599 1.032 0.992 0.201 3.356-2.611 100.00 3867 181 0.1299 256.680 255.244 1.029 0.986 0.101 2.608-2.000 99.99 8818 434 0.1351 167.311 165.504 1.039 0.977 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3934 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1652 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN B A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1275 r_free=0.1651 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1651 | n_water=258 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1279 r_free=0.1640 | n_water=254 | time (s): 20.590 (total time: 21.390) Filter (q & B) r_work=0.1280 r_free=0.1640 | n_water=252 | time (s): 1.940 (total time: 23.330) Compute maps r_work=0.1280 r_free=0.1640 | n_water=252 | time (s): 0.630 (total time: 23.960) Filter (map) r_work=0.1310 r_free=0.1627 | n_water=214 | time (s): 1.480 (total time: 25.440) Find peaks r_work=0.1310 r_free=0.1627 | n_water=214 | time (s): 0.430 (total time: 25.870) Add new water r_work=0.1531 r_free=0.1865 | n_water=373 | time (s): 1.640 (total time: 27.510) Refine new water occ: r_work=0.1326 r_free=0.1589 adp: r_work=0.1270 r_free=0.1576 occ: r_work=0.1274 r_free=0.1555 adp: r_work=0.1244 r_free=0.1556 occ: r_work=0.1245 r_free=0.1551 adp: r_work=0.1234 r_free=0.1549 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1549 r_work=0.1234 r_free=0.1549 | n_water=373 | time (s): 13.490 (total time: 41.000) Filter (q & B) r_work=0.1238 r_free=0.1557 | n_water=362 | time (s): 1.560 (total time: 42.560) Filter (dist only) r_work=0.1239 r_free=0.1558 | n_water=361 | time (s): 29.030 (total time: 71.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.440897 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.958539 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1214 0.1596 0.0381 0.008 0.9 1.9 0.5 0.0 0 12.720 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 15.96 3.81 4.176 21.164 0.959 0.018 12.00 16.21 4.20 4.197 21.323 0.959 0.018 Individual atomic B min max mean iso aniso Overall: 6.41 107.01 21.26 4.18 1888 0 Protein: 6.41 107.01 17.63 4.18 1519 0 Water: 8.73 68.14 36.42 N/A 361 0 Other: 22.41 37.58 27.73 N/A 8 0 Chain A: 6.41 107.01 19.39 N/A 1741 0 Chain S: 17.41 65.57 43.46 N/A 147 0 Histogram: Values Number of atoms 6.41 - 16.47 1013 16.47 - 26.53 388 26.53 - 36.59 224 36.59 - 46.65 146 46.65 - 56.71 82 56.71 - 66.77 24 66.77 - 76.83 4 76.83 - 86.89 4 86.89 - 96.95 1 96.95 - 107.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1621 r_work=0.1202 r_free=0.1625 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1625 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1618 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1194 r_free= 0.1618 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.017127 | | target function (ls_wunit_k1) not normalized (work): 278.049926 | | target function (ls_wunit_k1) not normalized (free): 24.975455 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1194 0.1618 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1752 0.1743 0.1968 n_refl.: 17042 remove outliers: r(all,work,free)=0.1752 0.1743 0.1968 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1728 0.1718 0.1952 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1190 0.1613 n_refl.: 17042 remove outliers: r(all,work,free)=0.1210 0.1189 0.1613 n_refl.: 17041 ======================== 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 0.3269 299.971 285.314 0.582 1.006 0.340 11.894-9.307 99.02 97 4 0.1540 487.537 484.047 0.906 1.006 0.340 9.237-7.194 100.00 213 7 0.1683 398.756 399.694 0.973 1.006 0.300 7.162-5.571 100.00 427 22 0.1565 299.267 295.410 0.936 1.006 0.281 5.546-4.326 100.00 867 58 0.0875 410.846 407.871 0.959 1.005 0.211 4.315-3.360 100.00 1859 96 0.0825 390.718 389.953 1.015 1.003 0.211 3.356-2.611 100.00 3867 181 0.1210 256.680 255.770 1.011 1.001 0.121 2.608-2.000 99.99 8818 434 0.1321 167.311 166.234 1.015 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3107 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1613 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=0.1190 r_free=0.1614 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1614 | n_water=361 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1191 r_free=0.1616 | n_water=360 | time (s): 29.030 (total time: 29.700) Filter (q & B) r_work=0.1191 r_free=0.1616 | n_water=360 | time (s): 0.940 (total time: 30.640) Compute maps r_work=0.1191 r_free=0.1616 | n_water=360 | time (s): 0.630 (total time: 31.270) Filter (map) r_work=0.1255 r_free=0.1637 | n_water=265 | time (s): 1.670 (total time: 32.940) Find peaks r_work=0.1255 r_free=0.1637 | n_water=265 | time (s): 0.470 (total time: 33.410) Add new water r_work=0.1443 r_free=0.1758 | n_water=405 | time (s): 1.720 (total time: 35.130) Refine new water occ: r_work=0.1245 r_free=0.1559 adp: r_work=0.1235 r_free=0.1558 occ: r_work=0.1221 r_free=0.1542 adp: r_work=0.1209 r_free=0.1537 occ: r_work=0.1205 r_free=0.1532 adp: r_work=0.1195 r_free=0.1532 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1532 r_work=0.1195 r_free=0.1532 | n_water=405 | time (s): 27.820 (total time: 62.950) Filter (q & B) r_work=0.1197 r_free=0.1538 | n_water=398 | time (s): 1.740 (total time: 64.690) Filter (dist only) r_work=0.1197 r_free=0.1542 | n_water=397 | time (s): 31.690 (total time: 96.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.939333 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.163806 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1167 0.1557 0.0389 0.009 1.0 2.9 0.5 0.0 0 0.970 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 15.57 3.89 4.277 21.403 0.164 4.996 11.48 15.54 4.06 4.856 21.320 0.164 4.973 Individual atomic B min max mean iso aniso Overall: 6.25 104.91 20.78 4.67 1924 0 Protein: 6.25 104.91 16.92 4.67 1519 0 Water: 8.93 60.68 35.33 N/A 397 0 Other: 23.72 39.95 30.60 N/A 8 0 Chain A: 6.25 104.91 18.68 N/A 1737 0 Chain S: 17.38 60.68 40.29 N/A 187 0 Histogram: Values Number of atoms 6.25 - 16.12 1069 16.12 - 25.98 342 25.98 - 35.85 210 35.85 - 45.72 183 45.72 - 55.58 79 55.58 - 65.45 28 65.45 - 75.31 5 75.31 - 85.18 3 85.18 - 95.04 3 95.04 - 104.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1148 r_free=0.1554 r_work=0.1148 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1148 r_free = 0.1554 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1556 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1142 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.970608 | | target function (ml) not normalized (work): 80692.847061 | | target function (ml) not normalized (free): 4191.612895 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1142 0.1556 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1673 0.1664 0.1893 n_refl.: 17041 remove outliers: r(all,work,free)=0.1673 0.1664 0.1893 n_refl.: 17041 overall B=-0.46 to atoms: r(all,work,free)=0.1642 0.1632 0.1877 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1162 0.1142 0.1559 n_refl.: 17041 remove outliers: r(all,work,free)=0.1162 0.1142 0.1559 n_refl.: 17041 ======================== 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 0.3538 299.971 277.949 0.566 1.006 0.340 11.894-9.307 99.02 97 4 0.1765 487.537 479.680 0.910 1.007 0.327 9.237-7.194 100.00 213 7 0.1785 398.756 399.582 0.986 1.007 0.277 7.162-5.571 100.00 427 22 0.1610 299.267 294.333 0.943 1.006 0.246 5.546-4.326 100.00 867 58 0.0932 410.846 407.261 0.965 1.005 0.211 4.315-3.360 100.00 1859 96 0.0888 390.718 388.800 1.011 1.003 0.195 3.356-2.611 100.00 3867 181 0.1261 256.680 254.606 1.011 1.000 0.162 2.608-2.000 99.99 8818 434 0.1097 167.311 165.903 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1659 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1559 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=0.1142 r_free=0.1556 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1556 | n_water=397 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1142 r_free=0.1556 | n_water=397 | time (s): 30.810 (total time: 31.550) Filter (q & B) r_work=0.1142 r_free=0.1556 | n_water=397 | time (s): 0.940 (total time: 32.490) Compute maps r_work=0.1142 r_free=0.1556 | n_water=397 | time (s): 0.780 (total time: 33.270) Filter (map) r_work=0.1196 r_free=0.1574 | n_water=308 | time (s): 2.060 (total time: 35.330) Find peaks r_work=0.1196 r_free=0.1574 | n_water=308 | time (s): 0.560 (total time: 35.890) Add new water r_work=0.1369 r_free=0.1689 | n_water=453 | time (s): 1.670 (total time: 37.560) Refine new water occ: r_work=0.1178 r_free=0.1492 adp: r_work=0.1170 r_free=0.1500 occ: r_work=0.1151 r_free=0.1478 adp: r_work=0.1141 r_free=0.1481 occ: r_work=0.1135 r_free=0.1476 adp: r_work=0.1126 r_free=0.1476 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1476 r_work=0.1126 r_free=0.1476 | n_water=453 | time (s): 32.980 (total time: 70.540) Filter (q & B) r_work=0.1128 r_free=0.1489 | n_water=443 | time (s): 1.520 (total time: 72.060) Filter (dist only) r_work=0.1128 r_free=0.1489 | n_water=443 | time (s): 32.330 (total time: 104.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.876324 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.172489 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1114 0.1544 0.0430 0.010 1.0 4.5 0.5 0.0 0 0.938 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.14 15.44 4.30 4.475 20.935 0.172 4.958 11.02 15.43 4.40 4.659 20.997 0.172 4.948 Individual atomic B min max mean iso aniso Overall: 5.57 102.33 20.95 4.94 1970 0 Protein: 5.57 102.33 16.44 4.93 1519 0 Water: 8.48 62.49 36.24 N/A 443 0 Other: 23.77 42.30 31.40 N/A 8 0 Chain A: 5.57 102.33 18.15 N/A 1736 0 Chain S: 16.75 62.49 41.75 N/A 234 0 Histogram: Values Number of atoms 5.57 - 15.25 1017 15.25 - 24.92 390 24.92 - 34.60 206 34.60 - 44.28 191 44.28 - 53.95 112 53.95 - 63.63 41 63.63 - 73.30 5 73.30 - 82.98 3 82.98 - 92.66 3 92.66 - 102.33 2 =========================== Idealize ADP of riding H ========================== r_work=0.1102 r_free=0.1543 r_work=0.1102 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1102 r_free = 0.1543 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1097 r_free = 0.1553 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1097 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.946268 | | target function (ml) not normalized (work): 80297.714592 | | target function (ml) not normalized (free): 4185.636836 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1097 0.1553 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1578 0.1563 0.1894 n_refl.: 17041 remove outliers: r(all,work,free)=0.1578 0.1563 0.1894 n_refl.: 17041 overall B=-0.28 to atoms: r(all,work,free)=0.1561 0.1545 0.1884 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1118 0.1096 0.1550 n_refl.: 17041 remove outliers: r(all,work,free)=0.1117 0.1095 0.1550 n_refl.: 17040 ======================== 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 93.75 85 5 0.3619 296.410 280.665 0.545 0.999 0.316 11.894-9.307 99.02 97 4 0.1760 487.537 479.422 0.919 1.001 0.307 9.237-7.194 100.00 213 7 0.1718 398.756 399.599 0.992 1.002 0.250 7.162-5.571 100.00 427 22 0.1566 299.267 293.906 0.947 1.002 0.220 5.546-4.326 100.00 867 58 0.0890 410.846 408.095 0.967 1.002 0.205 4.315-3.360 100.00 1859 96 0.0835 390.718 388.772 1.008 1.002 0.201 3.356-2.611 100.00 3867 181 0.1234 256.680 254.543 1.003 1.001 0.131 2.608-2.000 99.99 8818 434 0.1037 167.311 166.131 0.998 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9515 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1095 r_free=0.1550 After: r_work=0.1097 r_free=0.1548 ================================== NQH flips ================================== r_work=0.1097 r_free=0.1548 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1097 r_free=0.1548 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1097 r_free=0.1548 | n_water=443 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1097 r_free=0.1548 | n_water=443 | time (s): 34.110 (total time: 34.850) Filter (q & B) r_work=0.1097 r_free=0.1548 | n_water=442 | time (s): 2.040 (total time: 36.890) Compute maps r_work=0.1097 r_free=0.1548 | n_water=442 | time (s): 0.800 (total time: 37.690) Filter (map) r_work=0.1167 r_free=0.1573 | n_water=339 | time (s): 2.050 (total time: 39.740) Find peaks r_work=0.1167 r_free=0.1573 | n_water=339 | time (s): 0.580 (total time: 40.320) Add new water r_work=0.1297 r_free=0.1695 | n_water=481 | time (s): 1.910 (total time: 42.230) Refine new water occ: r_work=0.1138 r_free=0.1519 adp: r_work=0.1130 r_free=0.1520 occ: r_work=0.1119 r_free=0.1496 adp: r_work=0.1109 r_free=0.1496 occ: r_work=0.1104 r_free=0.1491 adp: r_work=0.1097 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1097 r_free=0.1487 r_work=0.1097 r_free=0.1487 | n_water=481 | time (s): 30.150 (total time: 72.380) Filter (q & B) r_work=0.1100 r_free=0.1500 | n_water=471 | time (s): 1.890 (total time: 74.270) Filter (dist only) r_work=0.1102 r_free=0.1496 | n_water=469 | time (s): 39.860 (total time: 114.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.040385 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.156724 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1116 0.1521 0.0405 0.011 1.1 5.1 0.5 0.0 0 1.020 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.21 4.05 4.581 20.788 0.157 4.946 11.07 15.10 4.03 4.613 20.815 0.157 4.935 Individual atomic B min max mean iso aniso Overall: 4.87 100.73 20.91 4.93 1996 0 Protein: 4.87 100.73 16.15 4.93 1519 0 Water: 8.18 62.72 36.14 N/A 469 0 Other: 23.41 41.07 30.80 N/A 8 0 Chain A: 4.87 100.73 17.82 N/A 1736 0 Chain S: 16.74 62.72 41.53 N/A 260 0 Histogram: Values Number of atoms 4.87 - 14.46 973 14.46 - 24.05 416 24.05 - 33.63 229 33.63 - 43.22 192 43.22 - 52.80 122 52.80 - 62.39 43 62.39 - 71.98 11 71.98 - 81.56 3 81.56 - 91.15 3 91.15 - 100.73 4 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1510 r_work=0.1106 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1509 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1512 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1512 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.932097 | | target function (ml) not normalized (work): 80062.736112 | | target function (ml) not normalized (free): 4162.579229 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1111 0.1380 5.4438 5.6442| | 2: 3.63 - 2.88 1.00 2711 122 0.1070 0.1441 5.2083 5.3268| | 3: 2.88 - 2.52 1.00 2681 148 0.1356 0.1801 5.1211 5.2219| | 4: 2.52 - 2.29 1.00 2661 139 0.0938 0.1551 4.6299 4.9589| | 5: 2.29 - 2.13 1.00 2678 122 0.0968 0.1417 4.5862 4.8641| | 6: 2.13 - 2.00 1.00 2692 117 0.1108 0.1703 4.5743 4.7839| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2810 159 0.95 8.95 1.00 0.95 6226.70| | 2: 3.63 - 2.88 2711 122 0.92 12.74 1.01 0.95 6226.70| | 3: 2.88 - 2.52 2681 148 0.88 18.76 0.99 0.95 6226.70| | 4: 2.52 - 2.29 2661 139 0.93 12.19 1.01 0.97 2147.83| | 5: 2.29 - 2.13 2678 122 0.91 14.21 1.00 0.97 2147.83| | 6: 2.13 - 2.00 2692 117 0.89 16.98 0.99 0.97 2147.83| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2147.83 max = 6226.70 mean = 4208.75| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.69 mean = 13.93| |phase err.(test): min = 0.00 max = 88.17 mean = 13.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1120 0.1100 0.1512 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1567 0.1554 0.1837 n_refl.: 17040 remove outliers: r(all,work,free)=0.1567 0.1554 0.1837 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1554 0.1541 0.1829 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1100 0.1511 n_refl.: 17040 remove outliers: r(all,work,free)=0.1120 0.1100 0.1511 n_refl.: 17040 ======================== 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 93.75 85 5 0.3653 296.410 277.400 0.541 1.003 0.329 11.894-9.307 99.02 97 4 0.1726 487.537 480.239 0.914 1.005 0.329 9.237-7.194 100.00 213 7 0.1717 398.756 398.887 0.988 1.005 0.244 7.162-5.571 100.00 427 22 0.1521 299.267 294.717 0.941 1.005 0.225 5.546-4.326 100.00 867 58 0.0917 410.846 407.629 0.963 1.004 0.211 4.315-3.360 100.00 1859 96 0.0869 390.718 388.221 1.003 1.003 0.201 3.356-2.611 100.00 3867 181 0.1235 256.680 254.180 0.999 1.001 0.131 2.608-2.000 99.99 8818 434 0.1031 167.311 166.030 0.992 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7741 ================= 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 : 0.2787 0.1869 0.082 5.270 8.8 119.3 19.9 258 0.000 1_bss: 0.1607 0.1682 0.082 5.270 8.4 118.9 19.5 258 0.000 1_settarget: 0.1607 0.1682 0.082 5.270 8.4 118.9 19.5 258 0.000 1_nqh: 0.1609 0.1687 0.082 5.270 8.4 118.9 19.5 258 0.009 1_weight: 0.1609 0.1687 0.082 5.270 8.4 118.9 19.5 258 0.009 1_xyzrec: 0.1354 0.1636 0.009 0.982 8.4 118.9 19.5 258 0.158 1_adp: 0.1277 0.1660 0.009 0.982 6.2 113.9 20.0 258 0.158 1_regHadp: 0.1280 0.1666 0.009 0.982 6.2 113.9 20.0 258 0.158 1_occ: 0.1274 0.1663 0.009 0.982 6.2 113.9 20.0 258 0.158 2_bss: 0.1273 0.1652 0.009 0.982 5.8 113.5 19.7 258 0.158 2_settarget: 0.1273 0.1652 0.009 0.982 5.8 113.5 19.7 258 0.158 2_updatecdl: 0.1273 0.1652 0.009 0.986 5.8 113.5 19.7 258 0.158 2_nqh: 0.1275 0.1651 0.009 0.986 5.8 113.5 19.7 258 0.149 2_sol: 0.1239 0.1558 0.009 0.986 5.8 112.0 21.0 361 n/a 2_weight: 0.1239 0.1558 0.009 0.986 5.8 112.0 21.0 361 n/a 2_xyzrec: 0.1214 0.1596 0.008 0.938 5.8 112.0 21.0 361 n/a 2_adp: 0.1200 0.1621 0.008 0.938 6.4 107.0 21.3 361 n/a 2_regHadp: 0.1202 0.1625 0.008 0.938 6.4 107.0 21.3 361 n/a 2_occ: 0.1194 0.1618 0.008 0.938 6.4 107.0 21.3 361 n/a 3_bss: 0.1189 0.1613 0.008 0.938 6.0 106.6 20.9 361 n/a 3_settarget: 0.1189 0.1613 0.008 0.938 6.0 106.6 20.9 361 n/a 3_updatecdl: 0.1189 0.1613 0.008 0.943 6.0 106.6 20.9 361 n/a 3_nqh: 0.1190 0.1614 0.008 0.943 6.0 106.6 20.9 361 n/a 3_sol: 0.1197 0.1542 0.008 0.943 6.0 106.6 20.9 397 n/a 3_weight: 0.1197 0.1542 0.008 0.943 6.0 106.6 20.9 397 n/a 3_xyzrec: 0.1167 0.1557 0.009 0.966 6.0 106.6 20.9 397 n/a 3_adp: 0.1148 0.1554 0.009 0.966 6.3 104.9 20.8 397 n/a 3_regHadp: 0.1148 0.1554 0.009 0.966 6.3 104.9 20.8 397 n/a 3_occ: 0.1142 0.1556 0.009 0.966 6.3 104.9 20.8 397 n/a 4_bss: 0.1142 0.1559 0.009 0.966 5.8 104.4 20.3 397 n/a 4_settarget: 0.1142 0.1559 0.009 0.966 5.8 104.4 20.3 397 n/a 4_updatecdl: 0.1142 0.1559 0.009 0.963 5.8 104.4 20.3 397 n/a 4_nqh: 0.1142 0.1556 0.009 0.963 5.8 104.4 20.3 397 n/a 4_sol: 0.1128 0.1489 0.009 0.963 5.8 104.4 20.8 443 n/a 4_weight: 0.1128 0.1489 0.009 0.963 5.8 104.4 20.8 443 n/a 4_xyzrec: 0.1114 0.1544 0.010 0.968 5.8 104.4 20.8 443 n/a 4_adp: 0.1102 0.1543 0.010 0.968 5.6 102.3 21.0 443 n/a 4_regHadp: 0.1102 0.1543 0.010 0.968 5.6 102.3 21.0 443 n/a 4_occ: 0.1097 0.1553 0.010 0.968 5.6 102.3 21.0 443 n/a 5_bss: 0.1095 0.1550 0.010 0.968 5.3 102.1 20.7 443 n/a 5_settarget: 0.1095 0.1550 0.010 0.968 5.3 102.1 20.7 443 n/a 5_updatecdl: 0.1095 0.1550 0.010 0.968 5.3 102.1 20.7 443 n/a 5_setrh: 0.1097 0.1548 0.010 0.968 5.3 102.1 20.7 443 n/a 5_nqh: 0.1097 0.1548 0.010 0.968 5.3 102.1 20.7 443 n/a 5_sol: 0.1102 0.1496 0.010 0.968 5.3 102.1 20.9 469 n/a 5_weight: 0.1102 0.1496 0.010 0.968 5.3 102.1 20.9 469 n/a 5_xyzrec: 0.1116 0.1521 0.011 1.058 5.3 102.1 20.9 469 n/a 5_adp: 0.1107 0.1510 0.011 1.058 4.9 100.7 20.9 469 n/a 5_regHadp: 0.1106 0.1509 0.011 1.058 4.9 100.7 20.9 469 n/a 5_occ: 0.1100 0.1512 0.011 1.058 4.9 100.7 20.9 469 n/a end: 0.1100 0.1511 0.011 1.058 4.7 100.5 20.7 469 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8736282_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8736282_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1400 Refinement macro-cycles (run) : 924.2600 Write final files (write_after_run_outputs) : 21.2000 Total : 948.6000 Total CPU time: 16.17 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:10 PST -0800 (1735494070.44 s) Start R-work = 0.1607, R-free = 0.1682 Final R-work = 0.1100, R-free = 0.1511 =============================================================================== Job complete usr+sys time: 993.01 seconds wall clock time: 16 minutes 55.31 seconds (1015.31 seconds total)