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_3675081.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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_3675081.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3675081.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.71, per 1000 atoms: 0.51 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 161.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.91: 511 0.91 - 1.15: 1100 1.15 - 1.38: 528 1.38 - 1.61: 887 1.61 - 1.85: 127 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 7 " pdb=" CA LEU A 7 " ideal model delta sigma weight residual 1.458 1.241 0.217 1.22e-02 6.72e+03 3.16e+02 bond pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.321 1.495 -0.174 1.00e-02 1.00e+04 3.04e+02 bond pdb=" C THR A 140 " pdb=" N TYR A 141 " ideal model delta sigma weight residual 1.330 1.091 0.239 1.38e-02 5.25e+03 3.00e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.235 1.430 -0.195 1.22e-02 6.72e+03 2.57e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.236 1.440 -0.204 1.29e-02 6.01e+03 2.51e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 3249 4.84 - 9.68: 1840 9.68 - 14.51: 603 14.51 - 19.35: 78 19.35 - 24.18: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 91 " pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 120.95 135.23 -14.28 1.04e+00 9.25e-01 1.89e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 134.83 -12.92 9.80e-01 1.04e+00 1.74e+02 angle pdb=" O BGLU A 94 " pdb=" C BGLU A 94 " pdb=" N GLN A 95 " ideal model delta sigma weight residual 122.15 136.82 -14.67 1.14e+00 7.69e-01 1.66e+02 angle pdb=" O ILE A 91 " pdb=" C ILE A 91 " pdb=" N LEU A 92 " ideal model delta sigma weight residual 121.87 109.39 12.48 9.70e-01 1.06e+00 1.66e+02 angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.61 136.53 -13.92 1.09e+00 8.42e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 1319 17.80 - 35.59: 109 35.59 - 53.38: 41 53.38 - 71.18: 8 71.18 - 88.97: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -140.07 17.47 0 2.50e+00 1.60e-01 4.88e+01 dihedral pdb=" C GLN A 180 " pdb=" N GLN A 180 " pdb=" CA GLN A 180 " pdb=" CB GLN A 180 " ideal model delta harmonic sigma weight residual -122.60 -105.52 -17.08 0 2.50e+00 1.60e-01 4.67e+01 dihedral pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CA BTYR A 67 " pdb=" CB BTYR A 67 " ideal model delta harmonic sigma weight residual 122.80 105.88 16.92 0 2.50e+00 1.60e-01 4.58e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.189: 94 0.189 - 0.375: 57 0.375 - 0.561: 52 0.561 - 0.746: 31 0.746 - 0.932: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" CB THR A 160 " pdb=" CA THR A 160 " pdb=" OG1 THR A 160 " pdb=" CG2 THR A 160 " both_signs ideal model delta sigma weight residual False 2.55 1.66 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.86 0.86 2.00e-01 2.50e+01 1.85e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.120 2.00e-02 2.50e+03 6.91e-02 1.43e+02 pdb=" CG ATYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.078 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.063 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.098 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.021 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.041 2.00e-02 2.50e+03 6.81e-02 1.39e+02 pdb=" CG PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.094 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.106 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.162 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.017 2.00e-02 2.50e+03 5.68e-02 9.68e+01 pdb=" CG TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.119 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.059 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 611 2.24 - 2.83: 7538 2.83 - 3.42: 10729 3.42 - 4.01: 15393 4.01 - 4.60: 22343 Nonbonded interactions: 56614 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.656 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.752 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.768 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.790 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.816 2.450 ... (remaining 56609 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_3675081_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= 0.3605 r_free= 0.2060 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463907 | | target function (ml) not normalized (work): 22007.059230 | | target function (ml) not normalized (free): 1151.426974 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3781 0.2267 4.8449 4.8942| | 2: 3.78 - 3.00 1.00 2430 110 0.3390 0.1709 4.072 4.1496| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.80 0.83 0.13 6599.19| | 2: 3.78 - 3.00 2430 110 0.94 11.22 1.48 0.26 439.94| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 376.47 max = 12075.16 mean = 3563.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.28| |phase err.(test): min = 0.00 max = 89.96 mean = 33.26| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.248 1557 Z= 5.357 Angle : 5.301 18.512 2118 Z= 3.705 Chirality : 0.382 0.932 243 Planarity : 0.033 0.090 284 Dihedral : 14.152 88.970 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.38 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 34.05 % 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: -1.90 (0.51), residues: 224 helix: -2.49 (0.38), residues: 103 sheet: -1.14 (0.76), residues: 28 loop : 0.60 (0.67), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.018 ARG A 28 TYR 0.124 0.036 TYR A 139 PHE 0.096 0.028 PHE A 164 HIS 0.086 0.041 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3605 r_free= 0.2060 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463907 | | target function (ml) not normalized (work): 22007.059230 | | target function (ml) not normalized (free): 1151.426974 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3562 0.3639 0.2152 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3562 0.3639 0.2152 n_refl.: 5182 remove outliers: r(all,work,free)=0.2513 0.2536 0.2152 n_refl.: 5178 overall B=-2.88 to atoms: r(all,work,free)=0.2404 0.2423 0.2106 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1564 0.1559 0.1648 n_refl.: 5178 remove outliers: r(all,work,free)=0.1562 0.1557 0.1648 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.3961 444.899 413.655 0.668 1.062 0.398 11.894-9.307 99.02 97 4 0.1906 714.231 692.057 0.947 1.059 0.383 9.237-7.194 100.00 213 7 0.2173 584.099 575.486 0.981 1.053 0.364 7.162-5.571 100.00 427 22 0.2330 438.295 424.572 0.944 1.041 0.347 5.546-4.326 100.00 867 58 0.1378 601.717 594.985 0.983 1.022 0.258 4.315-3.360 100.00 1859 96 0.1298 572.240 565.842 1.052 0.989 0.185 3.356-3.002 100.00 1373 60 0.1600 440.763 432.830 1.069 0.957 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.7014 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1557 r_free=0.1648 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 180 GLN Total number of N/Q/H flips: 2 r_work=0.1559 r_free=0.1643 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.900305 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.651605 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 0.1166 0.1817 0.0652 0.010 1.0 2.2 0.5 0.0 0 9.450 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 18.17 6.52 3.013 15.979 1.652 0.018 10.36 17.97 7.61 4.508 16.101 1.652 0.015 Individual atomic B min max mean iso aniso Overall: 2.30 111.42 17.24 4.94 1785 0 Protein: 2.30 110.94 14.53 4.93 1519 0 Water: 3.99 111.42 32.96 N/A 258 0 Other: 16.97 37.22 23.41 N/A 8 0 Chain A: 2.30 111.42 17.24 N/A 1785 0 Histogram: Values Number of atoms 2.30 - 13.21 945 13.21 - 24.12 469 24.12 - 35.03 180 35.03 - 45.95 106 45.95 - 56.86 55 56.86 - 67.77 13 67.77 - 78.68 8 78.68 - 89.59 5 89.59 - 100.51 1 100.51 - 111.42 3 =========================== Idealize ADP of riding H ========================== r_work=0.1036 r_free=0.1797 r_work=0.1029 r_free=0.1804 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1029 r_free = 0.1804 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1019 r_free = 0.1800 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1019 r_free= 0.1800 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014167 | | target function (ls_wunit_k1) not normalized (work): 69.771896 | | target function (ls_wunit_k1) not normalized (free): 10.320431 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1058 0.1019 0.1800 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2111 0.2112 0.2209 n_refl.: 5177 remove outliers: r(all,work,free)=0.2111 0.2112 0.2209 n_refl.: 5177 overall B=-0.98 to atoms: r(all,work,free)=0.2070 0.2069 0.2197 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1019 0.1788 n_refl.: 5177 remove outliers: r(all,work,free)=0.1056 0.1017 0.1788 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3446 324.192 309.125 0.661 1.012 0.370 11.894-9.307 99.02 97 4 0.1497 524.929 517.085 0.991 1.013 0.371 9.237-7.194 100.00 213 7 0.1633 429.288 430.245 1.025 1.012 0.326 7.162-5.571 100.00 427 22 0.1641 322.128 318.960 0.985 1.010 0.312 5.546-4.326 100.00 867 58 0.0916 442.237 439.533 0.998 1.005 0.232 4.315-3.360 100.00 1859 96 0.0764 420.572 420.280 1.040 0.998 0.187 3.356-3.002 100.00 1373 60 0.1015 323.942 322.417 1.021 0.991 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.4779 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1017 r_free=0.1788 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1018 r_free=0.1793 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1018 r_free=0.1793 | n_water=258 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1038 r_free=0.1774 | n_water=250 | time (s): 20.050 (total time: 20.650) Filter (q & B) r_work=0.1038 r_free=0.1774 | n_water=247 | time (s): 1.280 (total time: 21.930) Compute maps r_work=0.1038 r_free=0.1774 | n_water=247 | time (s): 0.560 (total time: 22.490) Filter (map) r_work=0.1327 r_free=0.1862 | n_water=146 | time (s): 1.440 (total time: 23.930) Find peaks r_work=0.1327 r_free=0.1862 | n_water=146 | time (s): 0.450 (total time: 24.380) Add new water r_work=0.1718 r_free=0.2205 | n_water=237 | time (s): 1.170 (total time: 25.550) Refine new water occ: r_work=0.1164 r_free=0.1665 adp: r_work=0.1137 r_free=0.1661 occ: r_work=0.1129 r_free=0.1637 adp: r_work=0.1116 r_free=0.1639 occ: r_work=0.1113 r_free=0.1632 adp: r_work=0.1109 r_free=0.1629 ADP+occupancy (water only), MIN, final r_work=0.1109 r_free=0.1629 r_work=0.1109 r_free=0.1629 | n_water=237 | time (s): 4.180 (total time: 29.730) Filter (q & B) r_work=0.1109 r_free=0.1629 | n_water=237 | time (s): 1.030 (total time: 30.760) Filter (dist only) r_work=0.1112 r_free=0.1633 | n_water=236 | time (s): 18.720 (total time: 49.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.678853 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.696461 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 0.1011 0.1742 0.0731 0.009 1.0 4.2 0.5 0.6 0 11.339 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.11 17.42 7.31 4.436 16.640 2.696 0.014 9.42 17.67 8.25 5.247 16.933 2.696 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.27 16.43 6.19 1763 0 Protein: 0.00 107.27 14.62 6.18 1519 0 Water: 0.00 63.27 27.91 N/A 236 0 Other: 10.99 33.20 21.92 N/A 8 0 Chain A: 0.00 107.27 15.39 N/A 1672 0 Chain S: 2.77 61.62 35.53 N/A 91 0 Histogram: Values Number of atoms 0.00 - 10.73 699 10.73 - 21.45 650 21.45 - 32.18 213 32.18 - 42.91 114 42.91 - 53.63 42 53.63 - 64.36 34 64.36 - 75.09 4 75.09 - 85.82 3 85.82 - 96.54 2 96.54 - 107.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.0942 r_free=0.1767 r_work=0.0939 r_free=0.1770 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0939 r_free = 0.1770 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0940 r_free = 0.1782 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.29 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= 0.0940 r_free= 0.1782 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012125 | | target function (ls_wunit_k1) not normalized (work): 59.702692 | | target function (ls_wunit_k1) not normalized (free): 9.822905 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0982 0.0940 0.1782 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2129 0.2131 0.2209 n_refl.: 5176 remove outliers: r(all,work,free)=0.2129 0.2131 0.2209 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2129 0.2131 0.2209 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0980 0.0938 0.1777 n_refl.: 5176 remove outliers: r(all,work,free)=0.0980 0.0938 0.1777 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 0.3392 324.192 309.914 0.645 1.010 0.360 11.894-9.307 99.02 97 4 0.1530 524.929 518.304 0.982 1.011 0.360 9.237-7.194 100.00 213 7 0.1461 429.288 430.119 1.024 1.010 0.310 7.162-5.571 100.00 427 22 0.1414 322.128 319.542 0.999 1.008 0.300 5.546-4.326 100.00 867 58 0.0797 442.237 440.323 1.009 1.005 0.250 4.315-3.360 100.00 1859 96 0.0723 420.572 420.480 1.051 0.999 0.203 3.356-3.002 100.00 1373 60 0.0956 323.942 322.759 1.034 0.993 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.1177 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0938 r_free=0.1777 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=0.0942 r_free=0.1782 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0942 r_free=0.1782 | n_water=236 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0952 r_free=0.1776 | n_water=231 | time (s): 17.260 (total time: 17.840) Filter (q & B) r_work=0.1007 r_free=0.1793 | n_water=229 | time (s): 1.890 (total time: 19.730) Compute maps r_work=0.1007 r_free=0.1793 | n_water=229 | time (s): 0.520 (total time: 20.250) Filter (map) r_work=0.1268 r_free=0.1855 | n_water=151 | time (s): 1.720 (total time: 21.970) Find peaks r_work=0.1268 r_free=0.1855 | n_water=151 | time (s): 0.410 (total time: 22.380) Add new water r_work=0.1638 r_free=0.2186 | n_water=230 | time (s): 1.290 (total time: 23.670) Refine new water occ: r_work=0.1062 r_free=0.1763 adp: r_work=0.1055 r_free=0.1776 occ: r_work=0.1045 r_free=0.1755 adp: r_work=0.1045 r_free=0.1755 occ: r_work=0.1045 r_free=0.1755 adp: r_work=0.1045 r_free=0.1755 ADP+occupancy (water only), MIN, final r_work=0.1045 r_free=0.1755 r_work=0.1045 r_free=0.1755 | n_water=230 | time (s): 8.560 (total time: 32.230) Filter (q & B) r_work=0.1045 r_free=0.1755 | n_water=230 | time (s): 1.020 (total time: 33.250) Filter (dist only) r_work=0.1057 r_free=0.1757 | n_water=228 | time (s): 17.420 (total time: 50.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.115434 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.243247 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 0.0949 0.1793 0.0844 0.011 1.1 5.8 0.5 0.6 0 0.558 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.49 17.93 8.44 5.200 17.228 0.243 5.172 9.02 18.09 9.07 7.143 17.244 0.243 5.076 Individual atomic B min max mean iso aniso Overall: 0.00 107.40 15.84 8.83 1755 0 Protein: 0.00 107.40 14.78 8.82 1519 0 Water: 0.00 58.27 22.62 N/A 228 0 Other: 10.88 35.68 22.00 N/A 8 0 Chain A: 0.00 107.40 15.47 N/A 1660 0 Chain S: 0.00 46.35 22.21 N/A 95 0 Histogram: Values Number of atoms 0.00 - 10.74 709 10.74 - 21.48 641 21.48 - 32.22 237 32.22 - 42.96 107 42.96 - 53.70 32 53.70 - 64.44 13 64.44 - 75.18 7 75.18 - 85.92 5 85.92 - 96.66 2 96.66 - 107.40 2 =========================== Idealize ADP of riding H ========================== r_work=0.0902 r_free=0.1809 r_work=0.0907 r_free=0.1821 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0907 r_free = 0.1821 target_work(ml) = 5.079 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0901 r_free = 0.1808 target_work(ml) = 5.074 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0901 r_free= 0.1808 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.073939 | | target function (ml) not normalized (work): 24984.075738 | | target function (ml) not normalized (free): 1839.714651 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0947 0.0901 0.1808 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2140 0.2152 0.2107 n_refl.: 5176 remove outliers: r(all,work,free)=0.2140 0.2152 0.2107 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2140 0.2152 0.2107 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0942 0.0896 0.1811 n_refl.: 5176 remove outliers: r(all,work,free)=0.0939 0.0893 0.1811 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3710 326.309 297.197 0.592 0.998 0.340 11.894-9.307 99.02 97 4 0.1898 524.929 509.000 0.949 1.001 0.330 9.237-7.194 100.00 213 7 0.1899 429.288 423.364 1.000 1.002 0.320 7.162-5.571 100.00 427 22 0.1797 322.128 314.511 0.979 1.003 0.300 5.546-4.326 100.00 867 58 0.0918 442.237 438.049 0.997 1.002 0.240 4.315-3.360 100.00 1859 96 0.0588 420.572 420.107 1.047 1.002 0.210 3.356-3.002 100.00 1373 60 0.0627 323.942 323.082 1.029 1.001 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.0662 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0893 r_free=0.1811 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=0.0894 r_free=0.1806 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0894 r_free=0.1806 | n_water=228 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0913 r_free=0.1807 | n_water=224 | time (s): 18.260 (total time: 18.810) Filter (q & B) r_work=0.0955 r_free=0.1835 | n_water=222 | time (s): 1.380 (total time: 20.190) Compute maps r_work=0.0955 r_free=0.1835 | n_water=222 | time (s): 0.520 (total time: 20.710) Filter (map) r_work=0.1219 r_free=0.1881 | n_water=160 | time (s): 1.650 (total time: 22.360) Find peaks r_work=0.1219 r_free=0.1881 | n_water=160 | time (s): 0.510 (total time: 22.870) Add new water r_work=0.1517 r_free=0.2204 | n_water=230 | time (s): 1.260 (total time: 24.130) Refine new water occ: r_work=0.1012 r_free=0.1782 adp: r_work=0.1008 r_free=0.1802 occ: r_work=0.0997 r_free=0.1776 adp: r_work=0.0998 r_free=0.1790 occ: r_work=0.0988 r_free=0.1763 adp: r_work=0.0988 r_free=0.1775 ADP+occupancy (water only), MIN, final r_work=0.0988 r_free=0.1775 r_work=0.0988 r_free=0.1775 | n_water=230 | time (s): 13.190 (total time: 37.320) Filter (q & B) r_work=0.0988 r_free=0.1775 | n_water=230 | time (s): 0.890 (total time: 38.210) Filter (dist only) r_work=0.0989 r_free=0.1784 | n_water=228 | time (s): 17.330 (total time: 55.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.997856 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.192529 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 0.0900 0.1891 0.0991 0.011 1.0 6.4 0.5 0.0 0 0.499 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.00 18.91 9.91 6.872 17.503 0.193 5.036 8.78 19.21 10.44 7.746 17.572 0.193 4.967 Individual atomic B min max mean iso aniso Overall: 0.00 107.15 16.16 10.04 1755 0 Protein: 0.00 107.15 15.09 10.05 1519 0 Water: 0.00 55.45 23.09 N/A 228 0 Other: 10.87 34.40 22.15 N/A 8 0 Chain A: 0.00 107.15 15.63 N/A 1649 0 Chain S: 0.00 55.00 24.40 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.72 704 10.72 - 21.43 629 21.43 - 32.15 246 32.15 - 42.86 110 42.86 - 53.58 32 53.58 - 64.29 17 64.29 - 75.01 7 75.01 - 85.72 5 85.72 - 96.44 4 96.44 - 107.15 1 =========================== Idealize ADP of riding H ========================== r_work=0.0878 r_free=0.1921 r_work=0.0881 r_free=0.1922 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0881 r_free = 0.1922 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0867 r_free = 0.1902 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0867 r_free= 0.1902 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.962609 | | target function (ml) not normalized (work): 24430.925147 | | target function (ml) not normalized (free): 2219.921639 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0920 0.0867 0.1902 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2103 0.2102 0.2255 n_refl.: 5175 remove outliers: r(all,work,free)=0.2103 0.2102 0.2255 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2103 0.2102 0.2255 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0918 0.0866 0.1898 n_refl.: 5175 remove outliers: r(all,work,free)=0.0918 0.0866 0.1898 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3767 326.309 301.320 0.589 0.988 0.327 11.894-9.307 99.02 97 4 0.1935 524.929 507.688 0.951 0.993 0.324 9.237-7.194 100.00 213 7 0.2073 429.288 419.673 1.006 0.996 0.310 7.162-5.571 100.00 427 22 0.1912 322.128 313.209 0.990 0.997 0.290 5.546-4.326 100.00 867 58 0.0974 442.237 437.008 1.011 0.999 0.240 4.315-3.360 100.00 1859 96 0.0540 420.572 420.180 1.064 1.002 0.220 3.356-3.002 100.00 1373 60 0.0468 323.942 323.677 1.048 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.9873 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0866 r_free=0.1898 After: r_work=0.0869 r_free=0.1898 ================================== NQH flips ================================== r_work=0.0869 r_free=0.1898 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0869 r_free=0.1896 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0869 r_free=0.1896 | n_water=228 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0881 r_free=0.1895 | n_water=224 | time (s): 17.330 (total time: 17.820) Filter (q & B) r_work=0.0988 r_free=0.1928 | n_water=221 | time (s): 1.310 (total time: 19.130) Compute maps r_work=0.0988 r_free=0.1928 | n_water=221 | time (s): 0.510 (total time: 19.640) Filter (map) r_work=0.1243 r_free=0.1941 | n_water=161 | time (s): 1.380 (total time: 21.020) Find peaks r_work=0.1243 r_free=0.1941 | n_water=161 | time (s): 0.450 (total time: 21.470) Add new water r_work=0.1520 r_free=0.2144 | n_water=227 | time (s): 1.240 (total time: 22.710) Refine new water occ: r_work=0.0985 r_free=0.1867 adp: r_work=0.0975 r_free=0.1873 occ: r_work=0.0971 r_free=0.1860 adp: r_work=0.0969 r_free=0.1866 occ: r_work=0.0966 r_free=0.1852 adp: r_work=0.0964 r_free=0.1858 ADP+occupancy (water only), MIN, final r_work=0.0964 r_free=0.1858 r_work=0.0964 r_free=0.1858 | n_water=227 | time (s): 12.240 (total time: 34.950) Filter (q & B) r_work=0.0964 r_free=0.1860 | n_water=226 | time (s): 1.520 (total time: 36.470) Filter (dist only) r_work=0.0964 r_free=0.1860 | n_water=226 | time (s): 16.010 (total time: 52.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.944803 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.244476 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 0.0906 0.1870 0.0964 0.010 1.1 8.3 0.5 0.0 0 0.472 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.06 18.70 9.64 7.677 17.784 0.244 5.013 8.87 18.84 9.98 8.609 17.889 0.244 4.956 Individual atomic B min max mean iso aniso Overall: 0.00 109.48 16.46 11.36 1753 0 Protein: 0.00 109.48 15.45 11.37 1519 0 Water: 0.00 61.13 23.04 N/A 226 0 Other: 10.64 33.20 22.58 N/A 8 0 Chain A: 0.00 109.48 15.98 N/A 1642 0 Chain S: 0.00 53.11 23.65 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.95 701 10.95 - 21.90 613 21.90 - 32.84 262 32.84 - 43.79 109 43.79 - 54.74 37 54.74 - 65.69 14 65.69 - 76.64 5 76.64 - 87.58 7 87.58 - 98.53 3 98.53 - 109.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.0887 r_free=0.1884 r_work=0.0891 r_free=0.1886 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0891 r_free = 0.1886 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0883 r_free = 0.1873 target_work(ml) = 4.956 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0883 r_free= 0.1873 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.956269 | | target function (ml) not normalized (work): 24399.712887 | | target function (ml) not normalized (free): 2276.616904 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1256 0.1834 5.5308 6.2634| | 2: 3.78 - 3.00 1.00 2430 110 0.0427 0.1938 4.3669 12.611| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.92 12.02 1.00 0.98 12807.17| | 2: 3.78 - 3.00 2430 110 0.99 1.92 1.00 1.00 929.57| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 600.12 max = 21415.07 mean = 6944.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.88 mean = 7.04| |phase err.(test): min = 0.00 max = 68.32 mean = 7.00| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0933 0.0883 0.1873 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2144 0.2146 0.2242 n_refl.: 5175 remove outliers: r(all,work,free)=0.2144 0.2146 0.2242 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2144 0.2146 0.2242 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0884 0.1874 n_refl.: 5175 remove outliers: r(all,work,free)=0.0934 0.0884 0.1874 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3934 326.309 288.825 0.566 0.986 0.319 11.894-9.307 99.02 97 4 0.1981 524.929 513.388 0.970 0.992 0.319 9.237-7.194 100.00 213 7 0.2121 429.288 421.315 1.018 0.995 0.300 7.162-5.571 100.00 427 22 0.1963 322.128 313.095 0.997 0.997 0.290 5.546-4.326 100.00 867 58 0.1038 442.237 435.940 1.018 0.999 0.240 4.315-3.360 100.00 1859 96 0.0557 420.572 420.513 1.082 1.002 0.230 3.356-3.002 100.00 1373 60 0.0421 323.942 323.225 1.066 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.7562 ================= 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 : 0.3605 0.2060 0.083 5.301 8.8 119.3 19.9 258 0.000 1_bss: 0.1557 0.1648 0.083 5.301 6.0 116.4 17.0 258 0.000 1_settarget: 0.1557 0.1648 0.083 5.301 6.0 116.4 17.0 258 0.000 1_nqh: 0.1559 0.1643 0.083 5.301 6.0 116.4 17.0 258 0.006 1_weight: 0.1559 0.1643 0.083 5.301 6.0 116.4 17.0 258 0.006 1_xyzrec: 0.1166 0.1817 0.010 0.979 6.0 116.4 17.0 258 0.215 1_adp: 0.1036 0.1797 0.010 0.979 2.3 111.4 17.2 258 0.215 1_regHadp: 0.1029 0.1804 0.010 0.979 2.3 111.4 17.2 258 0.215 1_occ: 0.1019 0.1800 0.010 0.979 2.3 111.4 17.2 258 0.215 2_bss: 0.1017 0.1788 0.010 0.979 1.3 110.4 16.3 258 0.215 2_settarget: 0.1017 0.1788 0.010 0.979 1.3 110.4 16.3 258 0.215 2_updatecdl: 0.1017 0.1788 0.010 0.999 1.3 110.4 16.3 258 0.215 2_nqh: 0.1018 0.1793 0.010 0.999 1.3 110.4 16.3 258 0.212 2_sol: 0.1112 0.1633 0.010 0.999 1.0 110.0 15.9 236 n/a 2_weight: 0.1112 0.1633 0.010 0.999 1.0 110.0 15.9 236 n/a 2_xyzrec: 0.1011 0.1742 0.009 0.976 1.0 110.0 15.9 236 n/a 2_adp: 0.0942 0.1767 0.009 0.976 0.0 107.3 16.4 236 n/a 2_regHadp: 0.0939 0.1770 0.009 0.976 0.0 107.3 16.4 236 n/a 2_occ: 0.0940 0.1782 0.009 0.976 0.0 107.3 16.4 236 n/a 3_bss: 0.0938 0.1777 0.009 0.976 0.0 107.3 16.4 236 n/a 3_settarget: 0.0938 0.1777 0.009 0.976 0.0 107.3 16.4 236 n/a 3_updatecdl: 0.0938 0.1777 0.009 0.984 0.0 107.3 16.4 236 n/a 3_nqh: 0.0942 0.1782 0.009 0.984 0.0 107.3 16.4 236 n/a 3_sol: 0.1057 0.1757 0.009 0.984 0.0 107.3 15.8 228 n/a 3_weight: 0.1057 0.1757 0.009 0.984 0.0 107.3 15.8 228 n/a 3_xyzrec: 0.0949 0.1793 0.011 1.076 0.0 107.3 15.8 228 n/a 3_adp: 0.0902 0.1809 0.011 1.076 0.0 107.4 15.8 228 n/a 3_regHadp: 0.0907 0.1821 0.011 1.076 0.0 107.4 15.8 228 n/a 3_occ: 0.0901 0.1808 0.011 1.076 0.0 107.4 15.8 228 n/a 4_bss: 0.0893 0.1811 0.011 1.076 0.0 107.4 15.8 228 n/a 4_settarget: 0.0893 0.1811 0.011 1.076 0.0 107.4 15.8 228 n/a 4_updatecdl: 0.0893 0.1811 0.011 1.085 0.0 107.4 15.8 228 n/a 4_nqh: 0.0894 0.1806 0.011 1.085 0.0 107.4 15.8 228 n/a 4_sol: 0.0989 0.1784 0.011 1.085 0.0 107.4 16.0 228 n/a 4_weight: 0.0989 0.1784 0.011 1.085 0.0 107.4 16.0 228 n/a 4_xyzrec: 0.0900 0.1891 0.011 1.046 0.0 107.4 16.0 228 n/a 4_adp: 0.0878 0.1921 0.011 1.046 0.0 107.2 16.2 228 n/a 4_regHadp: 0.0881 0.1922 0.011 1.046 0.0 107.2 16.2 228 n/a 4_occ: 0.0867 0.1902 0.011 1.046 0.0 107.2 16.2 228 n/a 5_bss: 0.0866 0.1898 0.011 1.046 0.0 107.2 16.2 228 n/a 5_settarget: 0.0866 0.1898 0.011 1.046 0.0 107.2 16.2 228 n/a 5_updatecdl: 0.0866 0.1898 0.011 1.048 0.0 107.2 16.2 228 n/a 5_setrh: 0.0869 0.1898 0.011 1.048 0.0 107.2 16.2 228 n/a 5_nqh: 0.0869 0.1896 0.011 1.048 0.0 107.2 16.2 228 n/a 5_sol: 0.0964 0.1860 0.011 1.048 0.0 107.2 16.3 226 n/a 5_weight: 0.0964 0.1860 0.011 1.048 0.0 107.2 16.3 226 n/a 5_xyzrec: 0.0906 0.1870 0.010 1.106 0.0 107.2 16.3 226 n/a 5_adp: 0.0887 0.1884 0.010 1.106 0.0 109.5 16.5 226 n/a 5_regHadp: 0.0891 0.1886 0.010 1.106 0.0 109.5 16.5 226 n/a 5_occ: 0.0883 0.1873 0.010 1.106 0.0 109.5 16.5 226 n/a end: 0.0884 0.1874 0.010 1.106 0.0 109.5 16.5 226 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3675081_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3675081_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8900 Refinement macro-cycles (run) : 479.1600 Write final files (write_after_run_outputs) : 11.6200 Total : 494.6700 Total CPU time: 8.64 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:59 PST -0800 (1735492739.09 s) Start R-work = 0.1557, R-free = 0.1648 Final R-work = 0.0884, R-free = 0.1874 =============================================================================== Job complete usr+sys time: 526.71 seconds wall clock time: 9 minutes 8.37 seconds (548.37 seconds total)