Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5637181.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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: 1.34, per 1000 atoms: 0.40 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: 0.31 Conformation dependent library (CDL) restraints added in 178.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.93: 646 0.93 - 1.19: 1017 1.19 - 1.45: 744 1.45 - 1.71: 729 1.71 - 1.97: 17 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.440 -0.205 9.90e-03 1.02e+04 4.27e+02 bond pdb=" N AGLU A 64 " pdb=" CA AGLU A 64 " ideal model delta sigma weight residual 1.457 1.680 -0.223 1.10e-02 8.26e+03 4.12e+02 bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.450 1.231 0.219 1.16e-02 7.43e+03 3.56e+02 bond pdb=" N GLU A 18 " pdb=" CA GLU A 18 " ideal model delta sigma weight residual 1.457 1.705 -0.248 1.32e-02 5.74e+03 3.54e+02 bond pdb=" CA AGLN A 80 " pdb=" C AGLN A 80 " ideal model delta sigma weight residual 1.524 1.759 -0.236 1.27e-02 6.20e+03 3.44e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 2872 4.14 - 8.29: 1875 8.29 - 12.43: 785 12.43 - 16.57: 219 16.57 - 20.71: 26 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 135.45 -16.25 9.00e-01 1.23e+00 3.26e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 106.11 13.09 9.00e-01 1.23e+00 2.11e+02 angle pdb=" O LEU A 112 " pdb=" C LEU A 112 " pdb=" N LEU A 113 " ideal model delta sigma weight residual 122.12 137.46 -15.34 1.06e+00 8.90e-01 2.09e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.36 137.31 -15.95 1.11e+00 8.12e-01 2.07e+02 angle pdb=" O LEU A 166 " pdb=" C LEU A 166 " pdb=" N ALA A 167 " ideal model delta sigma weight residual 122.12 107.57 14.55 1.06e+00 8.90e-01 1.88e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.51: 1306 16.51 - 33.00: 117 33.00 - 49.49: 38 49.49 - 65.99: 14 65.99 - 82.48: 6 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N LEU A 77 " pdb=" C LEU A 77 " pdb=" CA LEU A 77 " pdb=" CB LEU A 77 " ideal model delta harmonic sigma weight residual 122.80 141.47 -18.67 0 2.50e+00 1.60e-01 5.58e+01 dihedral pdb=" C GLU A 143 " pdb=" N GLU A 143 " pdb=" CA GLU A 143 " pdb=" CB GLU A 143 " ideal model delta harmonic sigma weight residual -122.60 -140.91 18.31 0 2.50e+00 1.60e-01 5.37e+01 dihedral pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual 123.40 140.85 -17.45 0 2.50e+00 1.60e-01 4.87e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.201: 100 0.201 - 0.400: 61 0.400 - 0.598: 49 0.598 - 0.797: 25 0.797 - 0.995: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.59 -1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CA THR A 154 " pdb=" N THR A 154 " pdb=" C THR A 154 " pdb=" CB THR A 154 " both_signs ideal model delta sigma weight residual False 2.53 3.51 -0.99 2.00e-01 2.50e+01 2.44e+01 chirality pdb=" CB VAL A 181 " pdb=" CA VAL A 181 " pdb=" CG1 VAL A 181 " pdb=" CG2 VAL A 181 " both_signs ideal model delta sigma weight residual False -2.63 -3.54 0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.111 2.00e-02 2.50e+03 6.02e-02 1.09e+02 pdb=" CG PHE A 164 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.117 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.099 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.073 2.00e-02 2.50e+03 5.56e-02 9.28e+01 pdb=" CG PHE A 119 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.116 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.061 2.00e-02 2.50e+03 5.49e-02 9.04e+01 pdb=" CG ATYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.001 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.095 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 810 2.28 - 2.86: 7854 2.86 - 3.44: 10597 3.44 - 4.02: 15300 4.02 - 4.60: 22047 Nonbonded interactions: 56608 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.702 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.723 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.800 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.834 2.450 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.842 2.450 ... (remaining 56603 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_5637181_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= 0.3615 r_free= 0.2019 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468121 | | target function (ml) not normalized (work): 22027.838430 | | target function (ml) not normalized (free): 1157.183154 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3792 0.2232 4.8542 4.9208| | 2: 3.78 - 3.00 1.00 2430 110 0.3399 0.1660 4.071 4.1675| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.84 0.83 0.13 6610.83| | 2: 3.78 - 3.00 2430 110 0.94 11.14 1.48 0.26 442.48| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 373.50 max = 12072.85 mean = 3570.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.97 mean = 30.26| |phase err.(test): min = 0.00 max = 89.91 mean = 33.04| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.249 1557 Z= 5.616 Angle : 5.384 16.340 2118 Z= 3.824 Chirality : 0.383 0.995 243 Planarity : 0.032 0.146 284 Dihedral : 14.086 82.483 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 39.46 % 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: -2.51 (0.48), residues: 224 helix: -2.56 (0.38), residues: 108 sheet: -0.55 (0.92), residues: 28 loop : -0.48 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.021 ARG A 98 TYR 0.141 0.047 TYR A 141 PHE 0.093 0.041 PHE A 119 HIS 0.072 0.035 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3615 r_free= 0.2019 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468121 | | target function (ml) not normalized (work): 22027.838430 | | target function (ml) not normalized (free): 1157.183154 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3570 0.3648 0.2128 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3570 0.3648 0.2128 n_refl.: 5182 remove outliers: r(all,work,free)=0.2527 0.2551 0.2128 n_refl.: 5178 overall B=-2.89 to atoms: r(all,work,free)=0.2416 0.2437 0.2094 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1571 0.1567 0.1666 n_refl.: 5178 remove outliers: r(all,work,free)=0.1567 0.1562 0.1666 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 0.3869 449.932 405.851 0.655 1.069 0.398 11.894-9.307 99.02 97 4 0.1931 714.753 693.928 0.944 1.065 0.383 9.237-7.194 100.00 213 7 0.2169 584.526 576.089 0.978 1.058 0.353 7.162-5.571 100.00 427 22 0.2339 438.616 424.214 0.936 1.045 0.295 5.546-4.326 100.00 867 58 0.1371 602.157 595.279 0.982 1.024 0.261 4.315-3.360 100.00 1859 96 0.1306 572.658 566.657 1.055 0.989 0.179 3.356-3.002 100.00 1373 60 0.1615 441.085 433.287 1.068 0.955 0.068 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6895 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1562 r_free=0.1666 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1562 r_free=0.1666 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.509312 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.837957 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 0.1165 0.1815 0.0650 0.009 1.0 2.6 0.5 0.0 0 9.255 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 18.15 6.50 3.013 15.973 1.838 0.018 10.26 18.10 7.84 4.863 16.164 1.838 0.015 Individual atomic B min max mean iso aniso Overall: 1.90 111.41 17.36 5.23 1785 0 Protein: 1.90 110.76 14.67 5.22 1519 0 Water: 3.98 111.41 32.99 N/A 258 0 Other: 17.18 37.71 24.10 N/A 8 0 Chain A: 1.90 111.41 17.36 N/A 1785 0 Histogram: Values Number of atoms 1.90 - 12.85 903 12.85 - 23.80 497 23.80 - 34.75 187 34.75 - 45.71 111 45.71 - 56.66 54 56.66 - 67.61 16 67.61 - 78.56 8 78.56 - 89.51 5 89.51 - 100.46 1 100.46 - 111.41 3 =========================== Idealize ADP of riding H ========================== r_work=0.1026 r_free=0.1810 r_work=0.1018 r_free=0.1815 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1018 r_free = 0.1815 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1016 r_free = 0.1815 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1016 r_free= 0.1815 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.014009 | | target function (ls_wunit_k1) not normalized (work): 68.978205 | | target function (ls_wunit_k1) not normalized (free): 10.860510 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1056 0.1016 0.1815 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2089 0.2086 0.2234 n_refl.: 5176 remove outliers: r(all,work,free)=0.2089 0.2086 0.2234 n_refl.: 5176 overall B=-0.98 to atoms: r(all,work,free)=0.2048 0.2044 0.2222 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1054 0.1014 0.1805 n_refl.: 5176 remove outliers: r(all,work,free)=0.1054 0.1014 0.1805 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 0.3305 330.574 311.117 0.665 1.016 0.376 11.894-9.307 99.02 97 4 0.1509 525.143 517.257 0.982 1.017 0.351 9.237-7.194 100.00 213 7 0.1722 429.463 428.320 1.015 1.015 0.310 7.162-5.571 100.00 427 22 0.1643 322.259 318.588 0.978 1.012 0.292 5.546-4.326 100.00 867 58 0.0915 442.417 439.189 0.996 1.007 0.222 4.315-3.360 100.00 1859 96 0.0759 420.743 420.592 1.044 0.997 0.183 3.356-3.002 100.00 1373 60 0.0999 324.074 322.762 1.022 0.989 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4938 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1014 r_free=0.1805 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1016 r_free=0.1806 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1016 r_free=0.1806 | n_water=258 | time (s): 0.450 (total time: 0.450) Filter (dist) r_work=0.1039 r_free=0.1803 | n_water=249 | time (s): 21.330 (total time: 21.780) Filter (q & B) r_work=0.1039 r_free=0.1803 | n_water=246 | time (s): 1.240 (total time: 23.020) Compute maps r_work=0.1039 r_free=0.1803 | n_water=246 | time (s): 0.530 (total time: 23.550) Filter (map) r_work=0.1364 r_free=0.1832 | n_water=143 | time (s): 1.510 (total time: 25.060) Find peaks r_work=0.1364 r_free=0.1832 | n_water=143 | time (s): 0.550 (total time: 25.610) Add new water r_work=0.1722 r_free=0.2152 | n_water=235 | time (s): 1.370 (total time: 26.980) Refine new water occ: r_work=0.1156 r_free=0.1698 adp: r_work=0.1133 r_free=0.1706 occ: r_work=0.1127 r_free=0.1676 adp: r_work=0.1115 r_free=0.1682 occ: r_work=0.1113 r_free=0.1672 adp: r_work=0.1110 r_free=0.1672 ADP+occupancy (water only), MIN, final r_work=0.1110 r_free=0.1672 r_work=0.1110 r_free=0.1672 | n_water=235 | time (s): 4.230 (total time: 31.210) Filter (q & B) r_work=0.1110 r_free=0.1672 | n_water=235 | time (s): 0.890 (total time: 32.100) Filter (dist only) r_work=0.1114 r_free=0.1661 | n_water=232 | time (s): 18.460 (total time: 50.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.161144 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.813581 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 0.1006 0.1754 0.0747 0.009 1.0 4.2 0.5 0.6 0 11.081 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.06 17.54 7.47 4.625 16.752 2.814 0.014 9.40 17.82 8.42 5.477 17.127 2.814 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 105.75 16.54 6.51 1759 0 Protein: 0.00 105.75 14.89 6.48 1519 0 Water: 0.00 62.80 27.04 N/A 232 0 Other: 11.21 37.74 24.54 N/A 8 0 Chain A: 0.00 105.75 15.69 N/A 1668 0 Chain S: 0.00 58.49 32.07 N/A 91 0 Histogram: Values Number of atoms 0.00 - 10.58 682 10.58 - 21.15 656 21.15 - 31.73 207 31.73 - 42.30 124 42.30 - 52.88 48 52.88 - 63.45 26 63.45 - 74.03 8 74.03 - 84.60 3 84.60 - 95.18 3 95.18 - 105.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.0940 r_free=0.1782 r_work=0.0938 r_free=0.1782 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0938 r_free = 0.1782 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0935 r_free = 0.1786 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.18 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= 0.0935 r_free= 0.1786 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011991 | | target function (ls_wunit_k1) not normalized (work): 59.041344 | | target function (ls_wunit_k1) not normalized (free): 9.974906 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0977 0.0935 0.1786 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2132 0.2135 0.2226 n_refl.: 5176 remove outliers: r(all,work,free)=0.2132 0.2135 0.2226 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2132 0.2135 0.2226 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0979 0.0937 0.1781 n_refl.: 5176 remove outliers: r(all,work,free)=0.0975 0.0933 0.1781 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 0.3206 329.970 307.804 0.660 1.007 0.360 11.894-9.307 99.02 97 4 0.1431 525.143 521.272 0.980 1.009 0.325 9.237-7.194 100.00 213 7 0.1473 429.463 430.070 1.025 1.009 0.300 7.162-5.571 100.00 427 22 0.1397 322.259 320.370 0.996 1.007 0.290 5.546-4.326 100.00 867 58 0.0770 442.417 439.851 1.010 1.004 0.250 4.315-3.360 100.00 1859 96 0.0721 420.743 420.424 1.054 1.000 0.200 3.356-3.002 100.00 1373 60 0.0985 324.074 322.919 1.034 0.995 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-4.2003 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0933 r_free=0.1781 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0934 r_free=0.1783 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0934 r_free=0.1783 | n_water=232 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0967 r_free=0.1752 | n_water=224 | time (s): 16.800 (total time: 17.350) Filter (q & B) r_work=0.1031 r_free=0.1786 | n_water=221 | time (s): 1.360 (total time: 18.710) Compute maps r_work=0.1031 r_free=0.1786 | n_water=221 | time (s): 0.490 (total time: 19.200) Filter (map) r_work=0.1300 r_free=0.1835 | n_water=146 | time (s): 1.990 (total time: 21.190) Find peaks r_work=0.1300 r_free=0.1835 | n_water=146 | time (s): 0.580 (total time: 21.770) Add new water r_work=0.1678 r_free=0.2201 | n_water=235 | time (s): 1.570 (total time: 23.340) Refine new water occ: r_work=0.1059 r_free=0.1756 adp: r_work=0.1054 r_free=0.1762 occ: r_work=0.1042 r_free=0.1747 adp: r_work=0.1042 r_free=0.1752 occ: r_work=0.1032 r_free=0.1737 adp: r_work=0.1031 r_free=0.1742 ADP+occupancy (water only), MIN, final r_work=0.1031 r_free=0.1742 r_work=0.1031 r_free=0.1742 | n_water=235 | time (s): 11.540 (total time: 34.880) Filter (q & B) r_work=0.1031 r_free=0.1742 | n_water=235 | time (s): 0.980 (total time: 35.860) Filter (dist only) r_work=0.1038 r_free=0.1745 | n_water=233 | time (s): 19.150 (total time: 55.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.128366 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.219347 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 0.0931 0.1818 0.0887 0.011 1.1 4.8 0.5 0.6 0 0.564 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.31 18.18 8.87 5.425 17.706 0.219 5.156 8.82 18.20 9.38 7.292 17.719 0.219 5.057 Individual atomic B min max mean iso aniso Overall: 0.00 102.83 16.33 8.98 1760 0 Protein: 0.00 102.83 15.05 8.95 1519 0 Water: 0.00 57.80 24.41 N/A 233 0 Other: 6.21 41.03 24.22 N/A 8 0 Chain A: 0.00 102.83 15.70 N/A 1650 0 Chain S: 0.00 56.15 25.68 N/A 110 0 Histogram: Values Number of atoms 0.00 - 10.28 657 10.28 - 20.57 648 20.57 - 30.85 240 30.85 - 41.13 124 41.13 - 51.42 48 51.42 - 61.70 21 61.70 - 71.98 10 71.98 - 82.27 6 82.27 - 92.55 3 92.55 - 102.83 3 =========================== Idealize ADP of riding H ========================== r_work=0.0882 r_free=0.1820 r_work=0.0887 r_free=0.1827 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0887 r_free = 0.1827 target_work(ml) = 5.061 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0876 r_free = 0.1808 target_work(ml) = 5.053 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0876 r_free= 0.1808 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.052908 | | target function (ml) not normalized (work): 24870.414758 | | target function (ml) not normalized (free): 1855.765326 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0923 0.0876 0.1808 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2039 0.2044 0.2098 n_refl.: 5174 remove outliers: r(all,work,free)=0.2039 0.2044 0.2098 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2039 0.2044 0.2098 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0916 0.0869 0.1800 n_refl.: 5174 remove outliers: r(all,work,free)=0.0916 0.0869 0.1800 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 0.3621 329.970 302.570 0.608 0.991 0.332 11.894-9.307 99.02 97 4 0.1696 525.143 510.529 0.950 0.996 0.320 9.237-7.194 100.00 213 7 0.1863 429.463 423.310 1.001 0.998 0.295 7.162-5.571 100.00 427 22 0.1736 322.259 313.991 0.981 0.999 0.283 5.546-4.326 100.00 867 58 0.0903 442.417 437.796 0.998 1.000 0.250 4.315-3.360 100.00 1859 96 0.0576 420.743 420.154 1.048 1.002 0.205 3.356-3.002 100.00 1373 60 0.0613 324.074 323.421 1.029 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.1659 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0869 r_free=0.1800 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=0.0870 r_free=0.1799 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0870 r_free=0.1799 | n_water=233 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.0886 r_free=0.1801 | n_water=230 | time (s): 19.110 (total time: 19.730) Filter (q & B) r_work=0.0922 r_free=0.1828 | n_water=228 | time (s): 1.490 (total time: 21.220) Compute maps r_work=0.0922 r_free=0.1828 | n_water=228 | time (s): 0.530 (total time: 21.750) Filter (map) r_work=0.1199 r_free=0.1916 | n_water=154 | time (s): 1.300 (total time: 23.050) Find peaks r_work=0.1199 r_free=0.1916 | n_water=154 | time (s): 0.380 (total time: 23.430) Add new water r_work=0.1536 r_free=0.2217 | n_water=236 | time (s): 1.260 (total time: 24.690) Refine new water occ: r_work=0.0996 r_free=0.1789 adp: r_work=0.0994 r_free=0.1793 occ: r_work=0.0983 r_free=0.1778 adp: r_work=0.0983 r_free=0.1787 occ: r_work=0.0974 r_free=0.1771 adp: r_work=0.0973 r_free=0.1780 ADP+occupancy (water only), MIN, final r_work=0.0973 r_free=0.1780 r_work=0.0973 r_free=0.1780 | n_water=236 | time (s): 14.790 (total time: 39.480) Filter (q & B) r_work=0.0973 r_free=0.1782 | n_water=235 | time (s): 1.370 (total time: 40.850) Filter (dist only) r_work=0.0986 r_free=0.1788 | n_water=231 | time (s): 17.760 (total time: 58.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.988974 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.202361 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 0.0904 0.1888 0.0985 0.011 1.0 4.8 0.5 0.0 0 0.494 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.04 18.88 9.85 6.986 17.871 0.202 5.045 8.82 18.99 10.17 8.099 17.972 0.202 4.983 Individual atomic B min max mean iso aniso Overall: 0.00 102.47 16.63 10.52 1758 0 Protein: 0.00 102.47 15.41 10.49 1519 0 Water: 0.00 55.74 24.36 N/A 231 0 Other: 8.16 41.96 24.13 N/A 8 0 Chain A: 0.00 102.47 15.99 N/A 1640 0 Chain S: 0.00 55.74 25.58 N/A 118 0 Histogram: Values Number of atoms 0.00 - 10.25 647 10.25 - 20.49 626 20.49 - 30.74 270 30.74 - 40.99 118 40.99 - 51.23 53 51.23 - 61.48 19 61.48 - 71.73 12 71.73 - 81.97 6 81.97 - 92.22 5 92.22 - 102.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.0882 r_free=0.1899 r_work=0.0886 r_free=0.1906 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0886 r_free = 0.1906 target_work(ml) = 4.988 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0874 r_free = 0.1897 target_work(ml) = 4.980 | | occupancies: max = 1.00 min = 0.20 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= 0.0874 r_free= 0.1897 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.979647 | | target function (ml) not normalized (work): 24509.823752 | | target function (ml) not normalized (free): 2115.127148 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0926 0.0874 0.1897 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2083 0.2084 0.2207 n_refl.: 5174 remove outliers: r(all,work,free)=0.2083 0.2084 0.2207 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2083 0.2084 0.2207 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0924 0.0872 0.1900 n_refl.: 5174 remove outliers: r(all,work,free)=0.0924 0.0872 0.1900 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 0.3710 329.970 299.147 0.601 0.988 0.328 11.894-9.307 99.02 97 4 0.1826 525.143 510.143 0.946 0.994 0.322 9.237-7.194 100.00 213 7 0.2087 429.463 420.401 0.997 0.997 0.308 7.162-5.571 100.00 427 22 0.1961 322.259 312.415 0.993 0.998 0.300 5.546-4.326 100.00 867 58 0.0959 442.417 437.339 1.007 1.000 0.250 4.315-3.360 100.00 1859 96 0.0561 420.743 420.452 1.067 1.002 0.211 3.356-3.002 100.00 1373 60 0.0469 324.074 323.348 1.050 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0120 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0872 r_free=0.1900 After: r_work=0.0875 r_free=0.1898 ================================== NQH flips ================================== r_work=0.0875 r_free=0.1898 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.0875 r_free=0.1898 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0875 r_free=0.1898 | n_water=231 | time (s): 0.450 (total time: 0.450) Filter (dist) r_work=0.0891 r_free=0.1898 | n_water=226 | time (s): 18.420 (total time: 18.870) Filter (q & B) r_work=0.0962 r_free=0.1887 | n_water=224 | time (s): 1.900 (total time: 20.770) Compute maps r_work=0.0962 r_free=0.1887 | n_water=224 | time (s): 0.510 (total time: 21.280) Filter (map) r_work=0.1245 r_free=0.1993 | n_water=154 | time (s): 1.570 (total time: 22.850) Find peaks r_work=0.1245 r_free=0.1993 | n_water=154 | time (s): 0.570 (total time: 23.420) Add new water r_work=0.1525 r_free=0.2234 | n_water=222 | time (s): 1.830 (total time: 25.250) Refine new water occ: r_work=0.1005 r_free=0.1856 adp: r_work=0.0998 r_free=0.1870 occ: r_work=0.0991 r_free=0.1856 adp: r_work=0.0990 r_free=0.1862 occ: r_work=0.0983 r_free=0.1850 adp: r_work=0.0983 r_free=0.1859 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1859 r_work=0.0983 r_free=0.1859 | n_water=222 | time (s): 12.230 (total time: 37.480) Filter (q & B) r_work=0.0983 r_free=0.1859 | n_water=221 | time (s): 1.420 (total time: 38.900) Filter (dist only) r_work=0.0987 r_free=0.1859 | n_water=220 | time (s): 16.180 (total time: 55.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.964661 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.233652 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 0.0929 0.1904 0.0974 0.011 1.1 6.7 0.5 0.0 0 0.482 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.29 19.04 9.74 8.011 18.174 0.234 5.041 9.08 18.89 9.80 9.007 18.233 0.234 4.988 Individual atomic B min max mean iso aniso Overall: 0.00 103.07 16.69 11.84 1747 0 Protein: 0.00 103.07 15.70 11.81 1519 0 Water: 0.00 58.42 23.25 N/A 220 0 Other: 7.53 40.30 24.61 N/A 8 0 Chain A: 0.00 103.07 16.17 N/A 1630 0 Chain S: 0.00 58.42 24.00 N/A 117 0 Histogram: Values Number of atoms 0.00 - 10.31 635 10.31 - 20.61 629 20.61 - 30.92 270 30.92 - 41.23 115 41.23 - 51.53 54 51.53 - 61.84 20 61.84 - 72.15 11 72.15 - 82.45 5 82.45 - 92.76 6 92.76 - 103.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.0908 r_free=0.1889 r_work=0.0912 r_free=0.1890 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1890 target_work(ml) = 4.994 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0901 r_free = 0.1885 target_work(ml) = 4.987 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0901 r_free= 0.1885 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.987403 | | target function (ml) not normalized (work): 24547.997046 | | target function (ml) not normalized (free): 2188.837891 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1263 0.1864 5.5249 6.2705| | 2: 3.78 - 3.00 1.00 2430 110 0.0458 0.1920 4.4362 11.804| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.92 12.10 1.00 0.98 13040.76| | 2: 3.78 - 3.00 2430 110 0.99 2.17 1.00 1.01 1045.26| |alpha: min = 0.97 max = 1.01 mean = 0.99| |beta: min = 700.94 max = 21925.78 mean = 7118.56| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.75 mean = 7.20| |phase err.(test): min = 0.00 max = 84.28 mean = 7.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0950 0.0901 0.1885 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2142 0.2144 0.2246 n_refl.: 5174 remove outliers: r(all,work,free)=0.2142 0.2144 0.2246 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2142 0.2144 0.2246 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0947 0.0899 0.1881 n_refl.: 5174 remove outliers: r(all,work,free)=0.0947 0.0899 0.1881 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 0.3783 329.970 297.592 0.631 0.987 0.345 11.894-9.307 99.02 97 4 0.1826 525.143 511.737 0.966 0.994 0.325 9.237-7.194 100.00 213 7 0.2216 429.463 418.347 0.993 0.997 0.301 7.162-5.571 100.00 427 22 0.2072 322.259 311.144 0.990 0.998 0.293 5.546-4.326 100.00 867 58 0.1035 442.417 436.786 1.008 1.000 0.240 4.315-3.360 100.00 1859 96 0.0569 420.743 420.347 1.081 1.002 0.219 3.356-3.002 100.00 1373 60 0.0440 324.074 323.553 1.067 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6627 ================= 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 : 0.3615 0.2019 0.084 5.384 8.8 119.3 19.9 258 0.000 1_bss: 0.1562 0.1666 0.084 5.384 6.0 116.4 17.0 258 0.000 1_settarget: 0.1562 0.1666 0.084 5.384 6.0 116.4 17.0 258 0.000 1_nqh: 0.1562 0.1666 0.084 5.384 6.0 116.4 17.0 258 0.000 1_weight: 0.1562 0.1666 0.084 5.384 6.0 116.4 17.0 258 0.000 1_xyzrec: 0.1165 0.1815 0.009 0.964 6.0 116.4 17.0 258 0.212 1_adp: 0.1026 0.1810 0.009 0.964 1.9 111.4 17.4 258 0.212 1_regHadp: 0.1018 0.1815 0.009 0.964 1.9 111.4 17.4 258 0.212 1_occ: 0.1016 0.1815 0.009 0.964 1.9 111.4 17.4 258 0.212 2_bss: 0.1014 0.1805 0.009 0.964 0.9 110.4 16.4 258 0.212 2_settarget: 0.1014 0.1805 0.009 0.964 0.9 110.4 16.4 258 0.212 2_updatecdl: 0.1014 0.1805 0.010 0.996 0.9 110.4 16.4 258 0.212 2_nqh: 0.1016 0.1806 0.010 0.996 0.9 110.4 16.4 258 0.215 2_sol: 0.1114 0.1661 0.010 0.996 0.9 109.8 15.8 232 n/a 2_weight: 0.1114 0.1661 0.010 0.996 0.9 109.8 15.8 232 n/a 2_xyzrec: 0.1006 0.1754 0.009 0.964 0.9 109.8 15.8 232 n/a 2_adp: 0.0940 0.1782 0.009 0.964 0.0 105.8 16.5 232 n/a 2_regHadp: 0.0938 0.1782 0.009 0.964 0.0 105.8 16.5 232 n/a 2_occ: 0.0935 0.1786 0.009 0.964 0.0 105.8 16.5 232 n/a 3_bss: 0.0933 0.1781 0.009 0.964 0.0 105.8 16.5 232 n/a 3_settarget: 0.0933 0.1781 0.009 0.964 0.0 105.8 16.5 232 n/a 3_updatecdl: 0.0933 0.1781 0.009 0.968 0.0 105.8 16.5 232 n/a 3_nqh: 0.0934 0.1783 0.009 0.968 0.0 105.8 16.5 232 n/a 3_sol: 0.1038 0.1745 0.009 0.968 0.0 105.8 16.3 233 n/a 3_weight: 0.1038 0.1745 0.009 0.968 0.0 105.8 16.3 233 n/a 3_xyzrec: 0.0931 0.1818 0.011 1.064 0.0 105.8 16.3 233 n/a 3_adp: 0.0882 0.1820 0.011 1.064 0.0 102.8 16.3 233 n/a 3_regHadp: 0.0887 0.1827 0.011 1.064 0.0 102.8 16.3 233 n/a 3_occ: 0.0876 0.1808 0.011 1.064 0.0 102.8 16.3 233 n/a 4_bss: 0.0869 0.1800 0.011 1.064 0.0 102.8 16.3 233 n/a 4_settarget: 0.0869 0.1800 0.011 1.064 0.0 102.8 16.3 233 n/a 4_updatecdl: 0.0869 0.1800 0.011 1.077 0.0 102.8 16.3 233 n/a 4_nqh: 0.0870 0.1799 0.011 1.077 0.0 102.8 16.3 233 n/a 4_sol: 0.0986 0.1788 0.011 1.077 0.0 102.8 16.4 231 n/a 4_weight: 0.0986 0.1788 0.011 1.077 0.0 102.8 16.4 231 n/a 4_xyzrec: 0.0904 0.1888 0.011 1.038 0.0 102.8 16.4 231 n/a 4_adp: 0.0882 0.1899 0.011 1.038 0.0 102.5 16.6 231 n/a 4_regHadp: 0.0886 0.1906 0.011 1.038 0.0 102.5 16.6 231 n/a 4_occ: 0.0874 0.1897 0.011 1.038 0.0 102.5 16.6 231 n/a 5_bss: 0.0872 0.1900 0.011 1.038 0.0 102.5 16.6 231 n/a 5_settarget: 0.0872 0.1900 0.011 1.038 0.0 102.5 16.6 231 n/a 5_updatecdl: 0.0872 0.1900 0.011 1.042 0.0 102.5 16.6 231 n/a 5_setrh: 0.0875 0.1898 0.011 1.042 0.0 102.5 16.6 231 n/a 5_nqh: 0.0875 0.1898 0.011 1.042 0.0 102.5 16.6 231 n/a 5_sol: 0.0987 0.1859 0.011 1.042 0.0 102.5 16.6 220 n/a 5_weight: 0.0987 0.1859 0.011 1.042 0.0 102.5 16.6 220 n/a 5_xyzrec: 0.0929 0.1904 0.011 1.112 0.0 102.5 16.6 220 n/a 5_adp: 0.0908 0.1889 0.011 1.112 0.0 103.1 16.7 220 n/a 5_regHadp: 0.0912 0.1890 0.011 1.112 0.0 103.1 16.7 220 n/a 5_occ: 0.0901 0.1885 0.011 1.112 0.0 103.1 16.7 220 n/a end: 0.0899 0.1881 0.011 1.112 0.0 103.1 16.7 220 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5637181_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5637181_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5200 Refinement macro-cycles (run) : 483.5100 Write final files (write_after_run_outputs) : 10.5000 Total : 497.5300 Total CPU time: 8.63 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:59 PST -0800 (1735492739.07 s) Start R-work = 0.1562, R-free = 0.1666 Final R-work = 0.0899, R-free = 0.1881 =============================================================================== Job complete usr+sys time: 526.04 seconds wall clock time: 9 minutes 7.69 seconds (547.69 seconds total)