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_3495505.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_3495505.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3495505.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 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: 1.40, per 1000 atoms: 0.41 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: 0.32 Conformation dependent library (CDL) restraints added in 111.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.44 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: 636 0.93 - 1.19: 1040 1.19 - 1.45: 691 1.45 - 1.71: 768 1.71 - 1.97: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.461 1.271 0.191 9.20e-03 1.18e+04 4.29e+02 bond pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 1.330 1.574 -0.244 1.26e-02 6.30e+03 3.74e+02 bond pdb=" N BGLU A 64 " pdb=" CA BGLU A 64 " ideal model delta sigma weight residual 1.456 1.686 -0.230 1.22e-02 6.72e+03 3.55e+02 bond pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 1.238 1.455 -0.217 1.17e-02 7.31e+03 3.46e+02 bond pdb=" C BGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 1.335 1.556 -0.221 1.26e-02 6.30e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.07: 3311 5.07 - 10.15: 1882 10.15 - 15.22: 508 15.22 - 20.29: 73 20.29 - 25.36: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.27 141.39 -19.12 1.23e+00 6.61e-01 2.42e+02 angle pdb=" N ILE A 91 " pdb=" CA ILE A 91 " pdb=" C ILE A 91 " ideal model delta sigma weight residual 110.62 125.23 -14.61 1.02e+00 9.61e-01 2.05e+02 angle pdb=" N PRO A 43 " pdb=" CA PRO A 43 " pdb=" CB PRO A 43 " ideal model delta sigma weight residual 103.25 115.48 -12.23 8.80e-01 1.29e+00 1.93e+02 angle pdb=" C ILE A 21 " pdb=" N PRO A 22 " pdb=" CA PRO A 22 " ideal model delta sigma weight residual 119.19 104.58 14.61 1.06e+00 8.90e-01 1.90e+02 angle pdb=" O GLN A 95 " pdb=" C GLN A 95 " pdb=" N BGLU A 96 " ideal model delta sigma weight residual 122.27 105.71 16.56 1.23e+00 6.61e-01 1.81e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 1308 17.07 - 34.14: 118 34.14 - 51.21: 37 51.21 - 68.28: 16 68.28 - 85.35: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ILE A 21 " pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual -122.00 -146.75 24.75 0 2.50e+00 1.60e-01 9.80e+01 dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 146.95 -24.15 0 2.50e+00 1.60e-01 9.33e+01 dihedral pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual 123.40 145.58 -22.18 0 2.50e+00 1.60e-01 7.87e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 116 0.247 - 0.494: 69 0.494 - 0.741: 43 0.741 - 0.988: 12 0.988 - 1.236: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 69 " pdb=" N VAL A 69 " pdb=" C VAL A 69 " pdb=" CB VAL A 69 " both_signs ideal model delta sigma weight residual False 2.44 3.68 -1.24 2.00e-01 2.50e+01 3.82e+01 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 -1.43 -1.16 2.00e-01 2.50e+01 3.36e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.64e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.032 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG TYR A 141 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.125 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.096 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.062 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.060 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 172 " -0.051 2.00e-02 2.50e+03 9.56e-02 9.14e+01 pdb=" C LEU A 172 " 0.165 2.00e-02 2.50e+03 pdb=" O LEU A 172 " -0.062 2.00e-02 2.50e+03 pdb=" N ASN A 173 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.067 2.00e-02 2.50e+03 5.22e-02 8.16e+01 pdb=" CG BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.076 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.002 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.077 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1268 2.35 - 2.91: 8252 2.91 - 3.47: 10473 3.47 - 4.04: 15152 4.04 - 4.60: 21487 Nonbonded interactions: 56632 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.785 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.808 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.835 2.270 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.836 2.450 ... (remaining 56627 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_3495505_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= 0.3612 r_free= 0.2097 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474269 | | target function (ml) not normalized (work): 22058.145362 | | target function (ml) not normalized (free): 1157.031947 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3803 0.2344 4.8507 4.9465| | 2: 3.78 - 3.00 1.00 2430 110 0.3377 0.1677 4.087 4.1331| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.82 0.83 0.13 6608.98| | 2: 3.78 - 3.00 2430 110 0.94 11.40 1.48 0.26 457.12| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 392.50 max = 12076.17 mean = 3576.72| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.38| |phase err.(test): min = 0.00 max = 89.97 mean = 33.17| |-----------------------------------------------------------------------------| ----------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 0.278 1557 Z= 5.407 Angle : 5.466 19.351 2118 Z= 3.832 Chirality : 0.408 1.236 243 Planarity : 0.032 0.129 284 Dihedral : 13.528 85.348 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 33.51 % 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: -2.76 (0.48), residues: 224 helix: -2.98 (0.36), residues: 109 sheet: -0.21 (0.80), residues: 28 loop : -0.43 (0.61), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.022 ARG A 156 TYR 0.131 0.041 TYR A 141 PHE 0.124 0.029 PHE A 119 HIS 0.086 0.034 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3612 r_free= 0.2097 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474269 | | target function (ml) not normalized (work): 22058.145362 | | target function (ml) not normalized (free): 1157.031947 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3569 0.3644 0.2178 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3569 0.3644 0.2178 n_refl.: 5182 remove outliers: r(all,work,free)=0.2517 0.2538 0.2178 n_refl.: 5178 overall B=-2.86 to atoms: r(all,work,free)=0.2408 0.2426 0.2126 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1568 0.1565 0.1638 n_refl.: 5178 remove outliers: r(all,work,free)=0.1564 0.1560 0.1638 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 0.3860 449.650 406.304 0.675 1.050 0.398 11.894-9.307 99.02 97 4 0.1845 714.305 695.469 0.955 1.047 0.383 9.237-7.194 100.00 213 7 0.2169 584.160 575.362 0.985 1.042 0.362 7.162-5.571 100.00 427 22 0.2305 438.341 424.768 0.947 1.033 0.302 5.546-4.326 100.00 867 58 0.1384 601.780 595.779 0.990 1.018 0.258 4.315-3.360 100.00 1859 96 0.1311 572.299 566.269 1.049 0.993 0.189 3.356-3.002 100.00 1373 60 0.1609 440.809 432.957 1.053 0.968 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6576 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1560 r_free=0.1638 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1561 r_free=0.1638 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.691546 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.967156 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 0.1162 0.1787 0.0625 0.009 1.0 2.9 0.5 0.0 0 9.346 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 17.87 6.25 3.013 15.999 1.967 0.018 10.23 17.56 7.33 4.909 16.172 1.967 0.015 Individual atomic B min max mean iso aniso Overall: 1.96 112.18 17.35 5.31 1785 0 Protein: 1.96 112.18 14.66 5.31 1519 0 Water: 4.00 111.44 33.05 N/A 258 0 Other: 17.43 36.29 23.79 N/A 8 0 Chain A: 1.96 112.18 17.35 N/A 1785 0 Histogram: Values Number of atoms 1.96 - 12.98 909 12.98 - 24.00 485 24.00 - 35.03 191 35.03 - 46.05 115 46.05 - 57.07 54 57.07 - 68.09 15 68.09 - 79.12 7 79.12 - 90.14 5 90.14 - 101.16 1 101.16 - 112.18 3 =========================== Idealize ADP of riding H ========================== r_work=0.1023 r_free=0.1756 r_work=0.1017 r_free=0.1762 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1762 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 = 0.1010 r_free = 0.1767 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= 0.1010 r_free= 0.1767 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013959 | | target function (ls_wunit_k1) not normalized (work): 68.735895 | | target function (ls_wunit_k1) not normalized (free): 10.325038 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1048 0.1010 0.1767 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2090 0.2089 0.2213 n_refl.: 5176 remove outliers: r(all,work,free)=0.2090 0.2089 0.2213 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2050 0.2048 0.2201 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1048 0.1010 0.1762 n_refl.: 5176 remove outliers: r(all,work,free)=0.1048 0.1010 0.1762 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 0.3385 330.185 312.629 0.673 1.014 0.381 11.894-9.307 99.02 97 4 0.1489 524.526 516.059 0.981 1.015 0.361 9.237-7.194 100.00 213 7 0.1695 428.958 428.648 1.015 1.014 0.306 7.162-5.571 100.00 427 22 0.1633 321.881 317.600 0.976 1.011 0.292 5.546-4.326 100.00 867 58 0.0901 441.897 438.932 0.998 1.006 0.232 4.315-3.360 100.00 1859 96 0.0759 420.248 420.142 1.042 0.998 0.193 3.356-3.002 100.00 1373 60 0.1000 323.693 322.305 1.019 0.990 0.073 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4165 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1010 r_free=0.1762 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1010 r_free=0.1762 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1762 | n_water=258 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.1042 r_free=0.1768 | n_water=247 | time (s): 20.910 (total time: 21.410) Filter (q & B) r_work=0.1041 r_free=0.1766 | n_water=244 | time (s): 1.620 (total time: 23.030) Compute maps r_work=0.1041 r_free=0.1766 | n_water=244 | time (s): 0.480 (total time: 23.510) Filter (map) r_work=0.1333 r_free=0.1794 | n_water=144 | time (s): 1.470 (total time: 24.980) Find peaks r_work=0.1333 r_free=0.1794 | n_water=144 | time (s): 0.410 (total time: 25.390) Add new water r_work=0.1687 r_free=0.2132 | n_water=230 | time (s): 1.380 (total time: 26.770) Refine new water occ: r_work=0.1153 r_free=0.1727 adp: r_work=0.1134 r_free=0.1714 occ: r_work=0.1130 r_free=0.1709 adp: r_work=0.1121 r_free=0.1703 occ: r_work=0.1118 r_free=0.1699 adp: r_work=0.1116 r_free=0.1694 ADP+occupancy (water only), MIN, final r_work=0.1116 r_free=0.1694 r_work=0.1116 r_free=0.1694 | n_water=230 | time (s): 3.510 (total time: 30.280) Filter (q & B) r_work=0.1116 r_free=0.1694 | n_water=230 | time (s): 0.840 (total time: 31.120) Filter (dist only) r_work=0.1121 r_free=0.1688 | n_water=227 | time (s): 16.780 (total time: 47.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.574239 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.824920 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 0.1013 0.1867 0.0855 0.009 1.0 4.5 0.5 0.6 0 11.287 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.13 18.67 8.55 4.676 16.749 2.825 0.014 9.45 18.93 9.48 5.462 17.163 2.825 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 110.86 16.58 6.50 1754 0 Protein: 0.00 110.86 15.02 6.49 1519 0 Water: 0.00 62.94 26.87 N/A 227 0 Other: 11.47 32.09 21.23 N/A 8 0 Chain A: 0.00 110.86 15.69 N/A 1668 0 Chain S: 3.73 61.31 33.80 N/A 86 0 Histogram: Values Number of atoms 0.00 - 11.09 723 11.09 - 22.17 641 22.17 - 33.26 212 33.26 - 44.34 107 44.34 - 55.43 38 55.43 - 66.51 21 66.51 - 77.60 6 77.60 - 88.69 3 88.69 - 99.77 2 99.77 - 110.86 1 =========================== Idealize ADP of riding H ========================== r_work=0.0945 r_free=0.1893 r_work=0.0942 r_free=0.1890 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0942 r_free = 0.1890 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 = 0.0937 r_free = 0.1863 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= 0.0937 r_free= 0.1863 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011959 | | target function (ls_wunit_k1) not normalized (work): 58.887184 | | target function (ls_wunit_k1) not normalized (free): 10.307850 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0982 0.0937 0.1863 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2130 0.2127 0.2313 n_refl.: 5176 remove outliers: r(all,work,free)=0.2130 0.2127 0.2313 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2130 0.2127 0.2313 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0983 0.0937 0.1872 n_refl.: 5176 remove outliers: r(all,work,free)=0.0983 0.0937 0.1872 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 0.3248 330.185 315.796 0.691 1.012 0.381 11.894-9.307 99.02 97 4 0.1427 524.526 520.393 0.972 1.014 0.360 9.237-7.194 100.00 213 7 0.1485 428.958 431.180 1.010 1.013 0.300 7.162-5.571 100.00 427 22 0.1399 321.881 320.246 0.983 1.010 0.290 5.546-4.326 100.00 867 58 0.0796 441.897 439.134 1.004 1.005 0.255 4.315-3.360 100.00 1859 96 0.0721 420.248 419.759 1.049 0.998 0.203 3.356-3.002 100.00 1373 60 0.0972 323.693 322.654 1.029 0.990 0.074 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.8196 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0937 r_free=0.1871 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0937 r_free=0.1873 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0937 r_free=0.1873 | n_water=227 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.0957 r_free=0.1852 | n_water=220 | time (s): 18.160 (total time: 18.850) Filter (q & B) r_work=0.1037 r_free=0.1848 | n_water=217 | time (s): 1.650 (total time: 20.500) Compute maps r_work=0.1037 r_free=0.1848 | n_water=217 | time (s): 0.510 (total time: 21.010) Filter (map) r_work=0.1263 r_free=0.1859 | n_water=146 | time (s): 1.550 (total time: 22.560) Find peaks r_work=0.1263 r_free=0.1859 | n_water=146 | time (s): 0.470 (total time: 23.030) Add new water r_work=0.1661 r_free=0.2225 | n_water=229 | time (s): 1.620 (total time: 24.650) Refine new water occ: r_work=0.1065 r_free=0.1798 adp: r_work=0.1059 r_free=0.1816 occ: r_work=0.1045 r_free=0.1791 adp: r_work=0.1046 r_free=0.1803 occ: r_work=0.1035 r_free=0.1779 adp: r_work=0.1035 r_free=0.1789 ADP+occupancy (water only), MIN, final r_work=0.1035 r_free=0.1789 r_work=0.1035 r_free=0.1789 | n_water=229 | time (s): 7.440 (total time: 32.090) Filter (q & B) r_work=0.1036 r_free=0.1790 | n_water=228 | time (s): 1.300 (total time: 33.390) Filter (dist only) r_work=0.1047 r_free=0.1776 | n_water=226 | time (s): 17.680 (total time: 51.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.114861 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.196319 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 0.0950 0.1849 0.0899 0.011 1.1 4.5 0.5 0.6 0 0.557 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.50 18.49 8.99 5.423 17.756 0.196 5.163 9.03 18.34 9.31 7.103 17.736 0.196 5.069 Individual atomic B min max mean iso aniso Overall: 0.00 111.02 16.26 8.70 1753 0 Protein: 0.00 111.02 15.10 8.70 1519 0 Water: 0.00 57.77 23.75 N/A 226 0 Other: 14.57 34.98 23.27 N/A 8 0 Chain A: 0.00 111.02 15.74 N/A 1657 0 Chain S: 0.00 53.20 25.18 N/A 96 0 Histogram: Values Number of atoms 0.00 - 11.10 718 11.10 - 22.20 648 22.20 - 33.31 222 33.31 - 44.41 106 44.41 - 55.51 29 55.51 - 66.61 13 66.61 - 77.72 12 77.72 - 88.82 1 88.82 - 99.92 3 99.92 - 111.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.0903 r_free=0.1834 r_work=0.0907 r_free=0.1842 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0907 r_free = 0.1842 target_work(ml) = 5.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0892 r_free = 0.1819 target_work(ml) = 5.064 | | occupancies: max = 1.00 min = 0.29 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= 0.0892 r_free= 0.1819 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.063503 | | target function (ml) not normalized (work): 24932.690942 | | target function (ml) not normalized (free): 1807.174550 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0939 0.0892 0.1819 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2179 0.2185 0.2217 n_refl.: 5176 remove outliers: r(all,work,free)=0.2179 0.2185 0.2217 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2179 0.2185 0.2217 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0888 0.1800 n_refl.: 5176 remove outliers: r(all,work,free)=0.0930 0.0884 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 0.3581 329.582 299.311 0.611 0.998 0.342 11.894-9.307 99.02 97 4 0.1725 524.526 513.883 0.947 1.001 0.337 9.237-7.194 100.00 213 7 0.1938 428.958 424.903 0.993 1.002 0.295 7.162-5.571 100.00 427 22 0.1823 321.881 313.377 0.969 1.002 0.290 5.546-4.326 100.00 867 58 0.0908 441.897 437.212 0.999 1.002 0.240 4.315-3.360 100.00 1859 96 0.0575 420.248 419.638 1.053 1.001 0.220 3.356-3.002 100.00 1373 60 0.0630 323.693 322.380 1.029 1.000 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9175 b_overall=-6.1389 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0884 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=0.0885 r_free=0.1799 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0885 r_free=0.1799 | n_water=226 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0900 r_free=0.1808 | n_water=221 | time (s): 17.550 (total time: 18.080) Filter (q & B) r_work=0.0950 r_free=0.1827 | n_water=219 | time (s): 1.430 (total time: 19.510) Compute maps r_work=0.0950 r_free=0.1827 | n_water=219 | time (s): 0.480 (total time: 19.990) Filter (map) r_work=0.1210 r_free=0.1862 | n_water=158 | time (s): 1.230 (total time: 21.220) Find peaks r_work=0.1210 r_free=0.1862 | n_water=158 | time (s): 0.450 (total time: 21.670) Add new water r_work=0.1537 r_free=0.2077 | n_water=234 | time (s): 1.440 (total time: 23.110) Refine new water occ: r_work=0.0993 r_free=0.1719 adp: r_work=0.0988 r_free=0.1736 occ: r_work=0.0979 r_free=0.1716 adp: r_work=0.0978 r_free=0.1725 occ: r_work=0.0971 r_free=0.1708 adp: r_work=0.0970 r_free=0.1715 ADP+occupancy (water only), MIN, final r_work=0.0970 r_free=0.1715 r_work=0.0970 r_free=0.1715 | n_water=234 | time (s): 8.410 (total time: 31.520) Filter (q & B) r_work=0.0971 r_free=0.1716 | n_water=231 | time (s): 2.010 (total time: 33.530) Filter (dist only) r_work=0.0976 r_free=0.1716 | n_water=228 | time (s): 17.820 (total time: 51.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.996444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.238946 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 0.0894 0.1807 0.0913 0.011 1.0 4.5 0.5 0.6 0 0.498 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.94 18.07 9.13 6.804 17.882 0.239 5.026 8.71 18.52 9.81 8.212 17.999 0.239 4.962 Individual atomic B min max mean iso aniso Overall: 0.00 113.05 16.60 10.73 1755 0 Protein: 0.00 113.05 15.53 10.73 1519 0 Water: 0.00 55.00 23.40 N/A 228 0 Other: 13.46 37.24 25.43 N/A 8 0 Chain A: 0.00 113.05 16.03 N/A 1645 0 Chain S: 0.00 55.00 24.98 N/A 110 0 Histogram: Values Number of atoms 0.00 - 11.30 712 11.30 - 22.61 630 22.61 - 33.91 239 33.91 - 45.22 110 45.22 - 56.52 35 56.52 - 67.83 14 67.83 - 79.13 9 79.13 - 90.44 2 90.44 - 101.74 3 101.74 - 113.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.0871 r_free=0.1852 r_work=0.0876 r_free=0.1860 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0876 r_free = 0.1860 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0865 r_free = 0.1849 target_work(ml) = 4.960 | | occupancies: max = 1.00 min = 0.29 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= 0.0865 r_free= 0.1849 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.959864 | | target function (ml) not normalized (work): 24412.450395 | | target function (ml) not normalized (free): 2086.913402 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0914 0.0865 0.1849 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2109 0.2107 0.2263 n_refl.: 5174 remove outliers: r(all,work,free)=0.2109 0.2107 0.2263 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2109 0.2107 0.2263 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0913 0.0863 0.1847 n_refl.: 5174 remove outliers: r(all,work,free)=0.0913 0.0863 0.1847 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 0.3740 329.582 300.815 0.611 0.988 0.340 11.894-9.307 99.02 97 4 0.1897 524.526 511.995 0.948 0.993 0.340 9.237-7.194 100.00 213 7 0.2108 428.958 420.474 1.001 0.996 0.291 7.162-5.571 100.00 427 22 0.1961 321.881 312.011 0.976 0.997 0.277 5.546-4.326 100.00 867 58 0.0949 441.897 437.207 1.013 1.000 0.251 4.315-3.360 100.00 1859 96 0.0547 420.248 420.086 1.073 1.003 0.220 3.356-3.002 100.00 1373 60 0.0450 323.693 323.664 1.049 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.1685 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0863 r_free=0.1847 After: r_work=0.0866 r_free=0.1847 ================================== NQH flips ================================== r_work=0.0866 r_free=0.1847 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=0.0867 r_free=0.1849 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0867 r_free=0.1849 | n_water=228 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0890 r_free=0.1843 | n_water=222 | time (s): 18.120 (total time: 18.730) Filter (q & B) r_work=0.1018 r_free=0.1906 | n_water=218 | time (s): 1.340 (total time: 20.070) Compute maps r_work=0.1018 r_free=0.1906 | n_water=218 | time (s): 0.420 (total time: 20.490) Filter (map) r_work=0.1227 r_free=0.1939 | n_water=161 | time (s): 1.580 (total time: 22.070) Find peaks r_work=0.1227 r_free=0.1939 | n_water=161 | time (s): 0.580 (total time: 22.650) Add new water r_work=0.1497 r_free=0.2112 | n_water=226 | time (s): 1.660 (total time: 24.310) Refine new water occ: r_work=0.0990 r_free=0.1818 adp: r_work=0.0981 r_free=0.1820 occ: r_work=0.0975 r_free=0.1817 adp: r_work=0.0973 r_free=0.1816 occ: r_work=0.0967 r_free=0.1814 adp: r_work=0.0966 r_free=0.1814 ADP+occupancy (water only), MIN, final r_work=0.0966 r_free=0.1814 r_work=0.0966 r_free=0.1814 | n_water=226 | time (s): 9.730 (total time: 34.040) Filter (q & B) r_work=0.0966 r_free=0.1817 | n_water=223 | time (s): 1.240 (total time: 35.280) Filter (dist only) r_work=0.0966 r_free=0.1817 | n_water=223 | time (s): 15.130 (total time: 50.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.026528 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.192123 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 0.0898 0.1827 0.0929 0.011 1.1 7.0 0.5 0.6 0 0.513 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.98 18.27 9.29 8.155 18.309 0.192 5.009 8.82 18.18 9.36 8.609 18.365 0.192 4.955 Individual atomic B min max mean iso aniso Overall: 0.00 113.36 16.79 11.28 1750 0 Protein: 0.00 113.36 15.78 11.27 1519 0 Water: 0.00 57.47 23.41 N/A 223 0 Other: 9.28 37.89 24.55 N/A 8 0 Chain A: 0.00 113.36 16.23 N/A 1639 0 Chain S: 0.00 57.47 25.14 N/A 111 0 Histogram: Values Number of atoms 0.00 - 11.34 700 11.34 - 22.67 644 22.67 - 34.01 237 34.01 - 45.34 103 45.34 - 56.68 35 56.68 - 68.01 15 68.01 - 79.35 8 79.35 - 90.68 4 90.68 - 102.02 3 102.02 - 113.36 1 =========================== Idealize ADP of riding H ========================== r_work=0.0882 r_free=0.1818 r_work=0.0885 r_free=0.1813 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0885 r_free = 0.1813 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0880 r_free = 0.1809 target_work(ml) = 4.956 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0880 r_free= 0.1809 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.955651 | | target function (ml) not normalized (work): 24391.714757 | | target function (ml) not normalized (free): 2157.262878 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1246 0.1766 5.5302 6.1979| | 2: 3.78 - 3.00 1.00 2430 110 0.0433 0.1883 4.3664 11.611| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2492 142 0.92 12.00 1.00 0.98 12898.60| | 2: 3.78 - 3.00 2430 110 0.99 1.88 1.00 1.00 927.19| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 591.47 max = 21424.66 mean = 6988.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.88 mean = 7.00| |phase err.(test): min = 0.00 max = 86.85 mean = 7.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0927 0.0880 0.1809 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2133 0.2131 0.2278 n_refl.: 5174 remove outliers: r(all,work,free)=0.2133 0.2131 0.2278 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2133 0.2131 0.2278 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0924 0.0877 0.1812 n_refl.: 5174 remove outliers: r(all,work,free)=0.0924 0.0877 0.1812 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 0.3825 329.582 298.718 0.629 0.985 0.350 11.894-9.307 99.02 97 4 0.1758 524.526 511.036 0.966 0.991 0.350 9.237-7.194 100.00 213 7 0.2154 428.958 419.673 1.002 0.995 0.290 7.162-5.571 100.00 427 22 0.1980 321.881 312.491 0.978 0.997 0.290 5.546-4.326 100.00 867 58 0.1002 441.897 436.775 1.016 0.999 0.235 4.315-3.360 100.00 1859 96 0.0575 420.248 420.254 1.086 1.003 0.230 3.356-3.002 100.00 1373 60 0.0412 323.693 323.694 1.068 1.006 0.071 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8547 ================= 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 : 0.3612 0.2097 0.083 5.466 8.8 119.3 19.9 258 0.000 1_bss: 0.1560 0.1638 0.083 5.466 6.0 116.4 17.0 258 0.000 1_settarget: 0.1560 0.1638 0.083 5.466 6.0 116.4 17.0 258 0.000 1_nqh: 0.1561 0.1638 0.083 5.466 6.0 116.4 17.0 258 0.003 1_weight: 0.1561 0.1638 0.083 5.466 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1162 0.1787 0.009 0.961 6.0 116.4 17.0 258 0.211 1_adp: 0.1023 0.1756 0.009 0.961 2.0 112.2 17.4 258 0.211 1_regHadp: 0.1017 0.1762 0.009 0.961 2.0 112.2 17.4 258 0.211 1_occ: 0.1010 0.1767 0.009 0.961 2.0 112.2 17.4 258 0.211 2_bss: 0.1010 0.1762 0.009 0.961 1.0 111.2 16.4 258 0.211 2_settarget: 0.1010 0.1762 0.009 0.961 1.0 111.2 16.4 258 0.211 2_updatecdl: 0.1010 0.1762 0.009 0.990 1.0 111.2 16.4 258 0.211 2_nqh: 0.1010 0.1762 0.009 0.990 1.0 111.2 16.4 258 0.211 2_sol: 0.1121 0.1688 0.009 0.990 1.0 111.2 15.8 227 n/a 2_weight: 0.1121 0.1688 0.009 0.990 1.0 111.2 15.8 227 n/a 2_xyzrec: 0.1013 0.1867 0.009 0.958 1.0 111.2 15.8 227 n/a 2_adp: 0.0945 0.1893 0.009 0.958 0.0 110.9 16.6 227 n/a 2_regHadp: 0.0942 0.1890 0.009 0.958 0.0 110.9 16.6 227 n/a 2_occ: 0.0937 0.1863 0.009 0.958 0.0 110.9 16.6 227 n/a 3_bss: 0.0937 0.1871 0.009 0.958 0.0 110.9 16.6 227 n/a 3_settarget: 0.0937 0.1871 0.009 0.958 0.0 110.9 16.6 227 n/a 3_updatecdl: 0.0937 0.1871 0.009 0.965 0.0 110.9 16.6 227 n/a 3_nqh: 0.0937 0.1873 0.009 0.965 0.0 110.9 16.6 227 n/a 3_sol: 0.1047 0.1776 0.009 0.965 0.0 110.9 16.3 226 n/a 3_weight: 0.1047 0.1776 0.009 0.965 0.0 110.9 16.3 226 n/a 3_xyzrec: 0.0950 0.1849 0.011 1.059 0.0 110.9 16.3 226 n/a 3_adp: 0.0903 0.1834 0.011 1.059 0.0 111.0 16.3 226 n/a 3_regHadp: 0.0907 0.1842 0.011 1.059 0.0 111.0 16.3 226 n/a 3_occ: 0.0892 0.1819 0.011 1.059 0.0 111.0 16.3 226 n/a 4_bss: 0.0884 0.1800 0.011 1.059 0.0 111.0 16.3 226 n/a 4_settarget: 0.0884 0.1800 0.011 1.059 0.0 111.0 16.3 226 n/a 4_updatecdl: 0.0884 0.1800 0.011 1.064 0.0 111.0 16.3 226 n/a 4_nqh: 0.0885 0.1799 0.011 1.064 0.0 111.0 16.3 226 n/a 4_sol: 0.0976 0.1716 0.011 1.064 0.0 111.0 16.4 228 n/a 4_weight: 0.0976 0.1716 0.011 1.064 0.0 111.0 16.4 228 n/a 4_xyzrec: 0.0894 0.1807 0.011 1.025 0.0 111.0 16.4 228 n/a 4_adp: 0.0871 0.1852 0.011 1.025 0.0 113.0 16.6 228 n/a 4_regHadp: 0.0876 0.1860 0.011 1.025 0.0 113.0 16.6 228 n/a 4_occ: 0.0865 0.1849 0.011 1.025 0.0 113.0 16.6 228 n/a 5_bss: 0.0863 0.1847 0.011 1.025 0.0 113.0 16.6 228 n/a 5_settarget: 0.0863 0.1847 0.011 1.025 0.0 113.0 16.6 228 n/a 5_updatecdl: 0.0863 0.1847 0.011 1.032 0.0 113.0 16.6 228 n/a 5_setrh: 0.0866 0.1847 0.011 1.032 0.0 113.0 16.6 228 n/a 5_nqh: 0.0867 0.1849 0.011 1.032 0.0 113.0 16.6 228 n/a 5_sol: 0.0966 0.1817 0.011 1.032 0.0 113.0 16.7 223 n/a 5_weight: 0.0966 0.1817 0.011 1.032 0.0 113.0 16.7 223 n/a 5_xyzrec: 0.0898 0.1827 0.011 1.142 0.0 113.0 16.7 223 n/a 5_adp: 0.0882 0.1818 0.011 1.142 0.0 113.4 16.8 223 n/a 5_regHadp: 0.0885 0.1813 0.011 1.142 0.0 113.4 16.8 223 n/a 5_occ: 0.0880 0.1809 0.011 1.142 0.0 113.4 16.8 223 n/a end: 0.0877 0.1812 0.011 1.142 0.0 113.4 16.8 223 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3495505_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3495505_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8500 Refinement macro-cycles (run) : 469.0500 Write final files (write_after_run_outputs) : 11.9700 Total : 483.8700 Total CPU time: 8.44 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:47 PST -0800 (1735492727.41 s) Start R-work = 0.1560, R-free = 0.1638 Final R-work = 0.0877, R-free = 0.1812 =============================================================================== Job complete usr+sys time: 515.23 seconds wall clock time: 8 minutes 57.42 seconds (537.42 seconds total)