Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.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" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.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: 1.34, per 1000 atoms: 0.40 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 105.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 596 0.92 - 1.17: 1062 1.17 - 1.42: 635 1.42 - 1.67: 824 1.67 - 1.92: 36 Bond restraints: 3153 Sorted by residual: bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.456 1.697 -0.241 1.16e-02 7.43e+03 4.32e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.458 1.680 -0.222 1.18e-02 7.18e+03 3.55e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.237 1.025 0.211 1.17e-02 7.31e+03 3.26e+02 bond pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta sigma weight residual 1.459 1.231 0.227 1.28e-02 6.10e+03 3.15e+02 bond pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 1.522 1.308 0.214 1.26e-02 6.30e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 3141 4.52 - 9.04: 1848 9.04 - 13.56: 658 13.56 - 18.08: 115 18.08 - 22.61: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BLYS A 93 " pdb=" C BLYS A 93 " pdb=" N BGLU A 94 " ideal model delta sigma weight residual 122.03 106.01 16.02 1.04e+00 9.25e-01 2.37e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 105.70 13.50 9.00e-01 1.23e+00 2.25e+02 angle pdb=" O SER A 47 " pdb=" C SER A 47 " pdb=" N ARG A 48 " ideal model delta sigma weight residual 122.27 140.62 -18.35 1.23e+00 6.61e-01 2.23e+02 angle pdb=" CA ALA A 183 " pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 118.63 131.52 -12.89 9.20e-01 1.18e+00 1.96e+02 angle pdb=" CA VAL A 169 " pdb=" C VAL A 169 " pdb=" O VAL A 169 " ideal model delta sigma weight residual 121.41 106.99 14.42 1.04e+00 9.25e-01 1.92e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 16.93: 1296 16.93 - 33.83: 129 33.83 - 50.74: 39 50.74 - 67.64: 14 67.64 - 84.55: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 20 " pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta harmonic sigma weight residual -122.00 -146.70 24.70 0 2.50e+00 1.60e-01 9.76e+01 dihedral pdb=" C ALA A 39 " pdb=" N ALA A 39 " pdb=" CA ALA A 39 " pdb=" CB ALA A 39 " ideal model delta harmonic sigma weight residual -122.60 -144.65 22.05 0 2.50e+00 1.60e-01 7.78e+01 dihedral pdb=" N VAL A 20 " pdb=" C VAL A 20 " pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta harmonic sigma weight residual 123.40 144.16 -20.76 0 2.50e+00 1.60e-01 6.90e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 126 0.270 - 0.541: 72 0.541 - 0.811: 33 0.811 - 1.081: 10 1.081 - 1.352: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 123 " pdb=" CA VAL A 123 " pdb=" CG1 VAL A 123 " pdb=" CG2 VAL A 123 " both_signs ideal model delta sigma weight residual False -2.63 -1.28 -1.35 2.00e-01 2.50e+01 4.57e+01 chirality pdb=" CA ALA A 39 " pdb=" N ALA A 39 " pdb=" C ALA A 39 " pdb=" CB ALA A 39 " both_signs ideal model delta sigma weight residual False 2.48 1.40 1.08 2.00e-01 2.50e+01 2.93e+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 -1.58 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.118 2.00e-02 2.50e+03 7.01e-02 1.48e+02 pdb=" CG PHE A 164 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.042 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.101 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.097 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.022 2.00e-02 2.50e+03 6.40e-02 1.23e+02 pdb=" CG BTYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.045 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.053 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.082 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.201 9.50e-02 1.11e+02 9.12e-02 9.07e+01 pdb=" NE ARG A 48 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " 0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " 0.073 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " -0.043 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.083 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.089 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 736 2.27 - 2.86: 7847 2.86 - 3.44: 10631 3.44 - 4.02: 15351 4.02 - 4.60: 22092 Nonbonded interactions: 56657 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.693 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.775 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.804 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.829 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.836 2.450 ... (remaining 56652 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_2780949_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= 0.3627 r_free= 0.2034 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468803 | | target function (ml) not normalized (work): 22031.196730 | | target function (ml) not normalized (free): 1148.886558 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3820 0.2196 4.8501 4.8947| | 2: 3.78 - 3.00 1.00 2430 110 0.3393 0.1761 4.0766 4.1258| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.90 0.83 0.13 6618.62| | 2: 3.78 - 3.00 2430 110 0.94 11.32 1.48 0.26 449.80| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 379.30 max = 12073.88 mean = 3578.01| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.37| |phase err.(test): min = 0.00 max = 89.93 mean = 33.29| |-----------------------------------------------------------------------------| ----------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 0.241 1557 Z= 5.541 Angle : 5.357 19.115 2118 Z= 3.758 Chirality : 0.407 1.352 243 Planarity : 0.033 0.084 284 Dihedral : 14.093 84.545 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.11 % Allowed : 1.86 % Favored : 95.03 % Cbeta Deviations : 31.35 % 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: -2.57 (0.48), residues: 224 helix: -2.56 (0.41), residues: 102 sheet: -1.40 (0.82), residues: 28 loop : -0.45 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.106 0.021 ARG A 98 TYR 0.090 0.046 TYR A 141 PHE 0.105 0.036 PHE A 164 HIS 0.038 0.019 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2034 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468803 | | target function (ml) not normalized (work): 22031.196730 | | target function (ml) not normalized (free): 1148.886558 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3580 0.3657 0.2148 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3580 0.3657 0.2148 n_refl.: 5182 remove outliers: r(all,work,free)=0.2529 0.2553 0.2148 n_refl.: 5178 overall B=-2.40 to atoms: r(all,work,free)=0.2437 0.2459 0.2103 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1563 0.1562 0.1578 n_refl.: 5178 remove outliers: r(all,work,free)=0.1557 0.1556 0.1578 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 97.87 87 5 0.3931 443.827 402.662 0.617 1.069 0.381 11.894-9.307 99.02 97 4 0.1841 713.979 694.042 0.900 1.067 0.379 9.237-7.194 100.00 213 7 0.2168 583.893 575.638 0.933 1.060 0.363 7.162-5.571 100.00 427 22 0.2316 438.141 423.743 0.898 1.047 0.308 5.546-4.326 100.00 867 58 0.1358 601.505 594.460 0.953 1.026 0.267 4.315-3.360 100.00 1859 96 0.1311 572.038 566.190 1.021 0.989 0.177 3.356-3.002 100.00 1373 60 0.1610 440.607 433.174 1.039 0.953 0.079 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9177 b_overall=-4.1401 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1556 r_free=0.1578 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1556 r_free=0.1578 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.661284 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.714623 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 0.1158 0.1785 0.0628 0.009 1.0 3.5 0.5 0.0 0 9.331 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 17.85 6.28 3.013 16.460 1.715 0.018 10.24 17.82 7.58 4.776 16.619 1.715 0.015 Individual atomic B min max mean iso aniso Overall: 2.30 111.90 17.79 5.17 1785 0 Protein: 2.30 111.55 15.09 5.16 1519 0 Water: 4.47 111.90 33.48 N/A 258 0 Other: 18.51 37.94 24.60 N/A 8 0 Chain A: 2.30 111.90 17.79 N/A 1785 0 Histogram: Values Number of atoms 2.30 - 13.26 907 13.26 - 24.22 492 24.22 - 35.18 189 35.18 - 46.14 109 46.14 - 57.10 56 57.10 - 68.06 15 68.06 - 79.02 8 79.02 - 89.98 5 89.98 - 100.94 1 100.94 - 111.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1024 r_free=0.1782 r_work=0.1018 r_free=0.1785 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1018 r_free = 0.1785 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1014 r_free = 0.1780 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1014 r_free= 0.1780 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014011 | | target function (ls_wunit_k1) not normalized (work): 68.976845 | | target function (ls_wunit_k1) not normalized (free): 10.189306 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1053 0.1014 0.1780 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2028 0.2020 0.2231 n_refl.: 5175 remove outliers: r(all,work,free)=0.2028 0.2020 0.2231 n_refl.: 5175 overall B=-1.05 to atoms: r(all,work,free)=0.1986 0.1977 0.2219 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1051 0.1012 0.1782 n_refl.: 5175 remove outliers: r(all,work,free)=0.1051 0.1012 0.1782 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 0.3240 313.676 297.684 0.655 1.014 0.360 11.894-9.307 99.02 97 4 0.1556 504.605 495.747 0.978 1.015 0.351 9.237-7.194 100.00 213 7 0.1683 412.667 411.804 1.017 1.014 0.322 7.162-5.571 100.00 427 22 0.1646 309.657 305.670 0.979 1.011 0.304 5.546-4.326 100.00 867 58 0.0913 425.114 422.074 1.003 1.006 0.233 4.315-3.360 100.00 1859 96 0.0763 404.288 403.972 1.049 0.997 0.183 3.356-3.002 100.00 1373 60 0.0995 311.400 310.263 1.029 0.988 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.7652 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1782 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1012 r_free=0.1782 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1012 r_free=0.1782 | n_water=258 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.1042 r_free=0.1774 | n_water=247 | time (s): 20.150 (total time: 20.730) Filter (q & B) r_work=0.1043 r_free=0.1775 | n_water=244 | time (s): 1.300 (total time: 22.030) Compute maps r_work=0.1043 r_free=0.1775 | n_water=244 | time (s): 0.470 (total time: 22.500) Filter (map) r_work=0.1326 r_free=0.1851 | n_water=148 | time (s): 1.640 (total time: 24.140) Find peaks r_work=0.1326 r_free=0.1851 | n_water=148 | time (s): 0.600 (total time: 24.740) Add new water r_work=0.1674 r_free=0.2128 | n_water=239 | time (s): 1.790 (total time: 26.530) Refine new water occ: r_work=0.1146 r_free=0.1674 adp: r_work=0.1123 r_free=0.1674 occ: r_work=0.1120 r_free=0.1663 adp: r_work=0.1108 r_free=0.1666 occ: r_work=0.1106 r_free=0.1654 adp: r_work=0.1106 r_free=0.1654 ADP+occupancy (water only), MIN, final r_work=0.1106 r_free=0.1654 r_work=0.1106 r_free=0.1654 | n_water=239 | time (s): 4.030 (total time: 30.560) Filter (q & B) r_work=0.1106 r_free=0.1654 | n_water=239 | time (s): 0.820 (total time: 31.380) Filter (dist only) r_work=0.1113 r_free=0.1649 | n_water=235 | time (s): 17.890 (total time: 49.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.027735 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.485610 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 0.1008 0.1789 0.0781 0.009 1.0 4.8 0.5 0.6 0 11.014 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.08 17.89 7.81 4.617 17.052 2.486 0.014 9.41 18.28 8.87 5.312 17.378 2.486 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.52 16.64 6.24 1762 0 Protein: 0.00 107.52 15.06 6.21 1519 0 Water: 0.00 63.13 26.40 N/A 235 0 Other: 13.97 46.41 28.58 N/A 8 0 Chain A: 0.00 107.52 15.83 N/A 1672 0 Chain S: 6.78 58.97 31.62 N/A 90 0 Histogram: Values Number of atoms 0.00 - 10.75 670 10.75 - 21.50 687 21.50 - 32.26 204 32.26 - 43.01 125 43.01 - 53.76 41 53.76 - 64.51 22 64.51 - 75.27 7 75.27 - 86.02 1 86.02 - 96.77 3 96.77 - 107.52 2 =========================== Idealize ADP of riding H ========================== r_work=0.0941 r_free=0.1828 r_work=0.0938 r_free=0.1830 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0938 r_free = 0.1830 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0935 r_free = 0.1816 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0935 r_free= 0.1816 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.011988 | | target function (ls_wunit_k1) not normalized (work): 59.019184 | | target function (ls_wunit_k1) not normalized (free): 9.884492 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0980 0.0935 0.1816 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2051 0.2049 0.2176 n_refl.: 5175 remove outliers: r(all,work,free)=0.2051 0.2049 0.2176 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2051 0.2049 0.2176 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0979 0.0934 0.1825 n_refl.: 5175 remove outliers: r(all,work,free)=0.0979 0.0934 0.1825 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 0.3275 313.676 297.253 0.659 1.007 0.360 11.894-9.307 99.02 97 4 0.1551 504.605 497.333 0.973 1.010 0.341 9.237-7.194 100.00 213 7 0.1457 412.667 414.512 1.022 1.010 0.320 7.162-5.571 100.00 427 22 0.1435 309.657 306.755 0.993 1.008 0.310 5.546-4.326 100.00 867 58 0.0803 425.114 422.526 1.013 1.004 0.250 4.315-3.360 100.00 1859 96 0.0716 404.288 403.801 1.059 0.998 0.200 3.356-3.002 100.00 1373 60 0.0944 311.400 310.739 1.040 0.992 0.076 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.3760 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0934 r_free=0.1825 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=0.0935 r_free=0.1828 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0935 r_free=0.1828 | n_water=235 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.0946 r_free=0.1832 | n_water=232 | time (s): 20.260 (total time: 20.720) Filter (q & B) r_work=0.0999 r_free=0.1832 | n_water=230 | time (s): 1.500 (total time: 22.220) Compute maps r_work=0.0999 r_free=0.1832 | n_water=230 | time (s): 0.480 (total time: 22.700) Filter (map) r_work=0.1247 r_free=0.1960 | n_water=156 | time (s): 1.410 (total time: 24.110) Find peaks r_work=0.1247 r_free=0.1960 | n_water=156 | time (s): 0.410 (total time: 24.520) Add new water r_work=0.1629 r_free=0.2383 | n_water=246 | time (s): 1.320 (total time: 25.840) Refine new water occ: r_work=0.1073 r_free=0.1871 adp: r_work=0.1068 r_free=0.1891 occ: r_work=0.1055 r_free=0.1860 adp: r_work=0.1055 r_free=0.1875 occ: r_work=0.1043 r_free=0.1845 adp: r_work=0.1043 r_free=0.1858 ADP+occupancy (water only), MIN, final r_work=0.1043 r_free=0.1858 r_work=0.1043 r_free=0.1858 | n_water=246 | time (s): 13.610 (total time: 39.450) Filter (q & B) r_work=0.1043 r_free=0.1858 | n_water=246 | time (s): 1.160 (total time: 40.610) Filter (dist only) r_work=0.1049 r_free=0.1847 | n_water=243 | time (s): 18.870 (total time: 59.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.075297 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.199696 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 0.0942 0.1835 0.0893 0.011 1.0 5.4 0.5 0.0 0 0.538 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.42 18.35 8.93 5.262 17.898 0.200 5.116 8.96 18.39 9.43 6.929 17.864 0.200 5.018 Individual atomic B min max mean iso aniso Overall: 0.00 108.07 16.48 8.43 1770 0 Protein: 0.00 108.07 15.15 8.41 1519 0 Water: 0.00 61.77 24.34 N/A 243 0 Other: 13.08 49.16 29.85 N/A 8 0 Chain A: 0.00 108.07 15.82 N/A 1662 0 Chain S: 0.00 61.77 26.58 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.81 675 10.81 - 21.61 683 21.61 - 32.42 223 32.42 - 43.23 119 43.23 - 54.04 36 54.04 - 64.84 18 64.84 - 75.65 10 75.65 - 86.46 1 86.46 - 97.27 4 97.27 - 108.07 1 =========================== Idealize ADP of riding H ========================== r_work=0.0896 r_free=0.1839 r_work=0.0901 r_free=0.1843 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0901 r_free = 0.1843 target_work(ml) = 5.022 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0888 r_free = 0.1816 target_work(ml) = 5.015 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0888 r_free= 0.1816 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.015415 | | target function (ml) not normalized (work): 24690.888073 | | target function (ml) not normalized (free): 1762.645305 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0888 0.1816 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2042 0.2051 0.2039 n_refl.: 5175 remove outliers: r(all,work,free)=0.2042 0.2051 0.2039 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2042 0.2051 0.2039 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0924 0.0878 0.1804 n_refl.: 5175 remove outliers: r(all,work,free)=0.0924 0.0878 0.1804 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 0.3747 313.676 287.272 0.574 0.991 0.320 11.894-9.307 99.02 97 4 0.1953 504.605 489.859 0.949 0.996 0.310 9.237-7.194 100.00 213 7 0.1926 412.667 407.375 1.014 0.998 0.300 7.162-5.571 100.00 427 22 0.1828 309.657 301.477 0.985 0.999 0.300 5.546-4.326 100.00 867 58 0.0868 425.114 420.289 1.009 1.001 0.245 4.315-3.360 100.00 1859 96 0.0578 404.288 403.626 1.063 1.002 0.210 3.356-3.002 100.00 1373 60 0.0598 311.400 311.536 1.046 1.003 0.067 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.8780 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0878 r_free=0.1804 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=0.0878 r_free=0.1803 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0878 r_free=0.1803 | n_water=243 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.0892 r_free=0.1803 | n_water=240 | time (s): 19.120 (total time: 19.760) Filter (q & B) r_work=0.0966 r_free=0.1835 | n_water=238 | time (s): 1.790 (total time: 21.550) Compute maps r_work=0.0966 r_free=0.1835 | n_water=238 | time (s): 0.630 (total time: 22.180) Filter (map) r_work=0.1269 r_free=0.1944 | n_water=154 | time (s): 1.720 (total time: 23.900) Find peaks r_work=0.1269 r_free=0.1944 | n_water=154 | time (s): 0.560 (total time: 24.460) Add new water r_work=0.1564 r_free=0.2260 | n_water=236 | time (s): 1.480 (total time: 25.940) Refine new water occ: r_work=0.1004 r_free=0.1834 adp: r_work=0.0998 r_free=0.1841 occ: r_work=0.0990 r_free=0.1818 adp: r_work=0.0990 r_free=0.1829 occ: r_work=0.0982 r_free=0.1807 adp: r_work=0.0982 r_free=0.1818 ADP+occupancy (water only), MIN, final r_work=0.0982 r_free=0.1818 r_work=0.0982 r_free=0.1818 | n_water=236 | time (s): 11.840 (total time: 37.780) Filter (q & B) r_work=0.0982 r_free=0.1819 | n_water=235 | time (s): 1.420 (total time: 39.200) Filter (dist only) r_work=0.0995 r_free=0.1815 | n_water=234 | time (s): 18.250 (total time: 57.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.049457 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.244172 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 0.0903 0.1878 0.0975 0.011 1.0 6.1 0.5 0.0 0 0.525 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.03 18.78 9.75 6.625 17.870 0.244 5.000 8.75 18.96 10.21 7.939 17.992 0.244 4.929 Individual atomic B min max mean iso aniso Overall: 0.00 105.83 16.67 10.26 1761 0 Protein: 0.00 105.83 15.55 10.24 1519 0 Water: 0.00 53.13 23.49 N/A 234 0 Other: 12.53 51.16 30.07 N/A 8 0 Chain A: 0.00 105.83 16.15 N/A 1649 0 Chain S: 0.00 49.53 24.39 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.58 623 10.58 - 21.17 686 21.17 - 31.75 248 31.75 - 42.33 128 42.33 - 52.91 42 52.91 - 63.50 14 63.50 - 74.08 10 74.08 - 84.66 5 84.66 - 95.25 4 95.25 - 105.83 1 =========================== Idealize ADP of riding H ========================== r_work=0.0875 r_free=0.1896 r_work=0.0879 r_free=0.1896 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0879 r_free = 0.1896 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0871 r_free = 0.1883 target_work(ml) = 4.927 | | occupancies: max = 1.00 min = 0.17 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= 0.0871 r_free= 0.1883 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.927271 | | target function (ml) not normalized (work): 24256.954016 | | target function (ml) not normalized (free): 2051.749939 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0923 0.0871 0.1883 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2088 0.2089 0.2198 n_refl.: 5175 remove outliers: r(all,work,free)=0.2088 0.2089 0.2198 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2088 0.2089 0.2198 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0922 0.0871 0.1877 n_refl.: 5175 remove outliers: r(all,work,free)=0.0922 0.0871 0.1877 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 0.3830 313.676 277.322 0.559 0.987 0.314 11.894-9.307 99.02 97 4 0.1943 504.605 491.877 0.958 0.993 0.310 9.237-7.194 100.00 213 7 0.2132 412.667 406.356 1.020 0.996 0.295 7.162-5.571 100.00 427 22 0.2009 309.657 301.505 0.996 0.997 0.290 5.546-4.326 100.00 867 58 0.0945 425.114 419.736 1.019 0.999 0.230 4.315-3.360 100.00 1859 96 0.0543 404.288 404.102 1.085 1.002 0.220 3.356-3.002 100.00 1373 60 0.0461 311.400 311.037 1.066 1.005 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.7961 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0871 r_free=0.1877 After: r_work=0.0874 r_free=0.1874 ================================== NQH flips ================================== r_work=0.0874 r_free=0.1874 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0874 r_free=0.1874 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0874 r_free=0.1874 | n_water=234 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.0884 r_free=0.1884 | n_water=230 | time (s): 18.270 (total time: 18.770) Filter (q & B) r_work=0.0965 r_free=0.1933 | n_water=226 | time (s): 1.360 (total time: 20.130) Compute maps r_work=0.0965 r_free=0.1933 | n_water=226 | time (s): 0.540 (total time: 20.670) Filter (map) r_work=0.1249 r_free=0.1994 | n_water=156 | time (s): 1.420 (total time: 22.090) Find peaks r_work=0.1249 r_free=0.1994 | n_water=156 | time (s): 0.540 (total time: 22.630) Add new water r_work=0.1538 r_free=0.2209 | n_water=230 | time (s): 1.450 (total time: 24.080) Refine new water occ: r_work=0.0977 r_free=0.1873 adp: r_work=0.0968 r_free=0.1873 occ: r_work=0.0961 r_free=0.1860 adp: r_work=0.0961 r_free=0.1867 occ: r_work=0.0954 r_free=0.1851 adp: r_work=0.0953 r_free=0.1859 ADP+occupancy (water only), MIN, final r_work=0.0953 r_free=0.1859 r_work=0.0953 r_free=0.1859 | n_water=230 | time (s): 8.650 (total time: 32.730) Filter (q & B) r_work=0.0953 r_free=0.1862 | n_water=228 | time (s): 1.440 (total time: 34.170) Filter (dist only) r_work=0.0953 r_free=0.1862 | n_water=228 | time (s): 16.620 (total time: 50.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.903618 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.254675 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0901 0.1851 0.0950 0.010 1.1 9.3 0.5 0.0 0 0.452 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.01 18.51 9.50 7.830 18.212 0.255 4.952 8.85 18.56 9.71 8.965 18.359 0.255 4.904 Individual atomic B min max mean iso aniso Overall: 0.00 104.30 16.99 11.89 1755 0 Protein: 0.00 104.30 16.00 11.85 1519 0 Water: 0.00 59.95 23.13 N/A 228 0 Other: 10.78 51.85 29.83 N/A 8 0 Chain A: 0.00 104.30 16.52 N/A 1644 0 Chain S: 0.00 51.49 23.89 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.43 614 10.43 - 20.86 655 20.86 - 31.29 272 31.29 - 41.72 125 41.72 - 52.15 49 52.15 - 62.58 15 62.58 - 73.01 11 73.01 - 83.44 6 83.44 - 93.87 5 93.87 - 104.30 3 =========================== Idealize ADP of riding H ========================== r_work=0.0885 r_free=0.1856 r_work=0.0889 r_free=0.1861 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0889 r_free = 0.1861 target_work(ml) = 4.911 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0883 r_free = 0.1856 target_work(ml) = 4.905 | | 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= 0.1856 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.905437 | | target function (ml) not normalized (work): 24149.467463 | | target function (ml) not normalized (free): 2093.755332 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1258 0.1888 5.4929 6.1903| | 2: 3.78 - 3.00 1.00 2430 110 0.0425 0.1802 4.3027 11.043| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.91 12.31 1.00 0.93 12525.69| | 2: 3.78 - 3.00 2430 110 0.99 1.74 1.00 0.96 810.06| |alpha: min = 0.92 max = 0.96 mean = 0.94| |beta: min = 515.03 max = 21118.82 mean = 6742.84| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.88 mean = 7.10| |phase err.(test): min = 0.00 max = 83.65 mean = 7.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0932 0.0883 0.1856 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2137 0.2139 0.2230 n_refl.: 5175 remove outliers: r(all,work,free)=0.2137 0.2139 0.2230 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2137 0.2139 0.2230 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0931 0.0882 0.1856 n_refl.: 5175 remove outliers: r(all,work,free)=0.0931 0.0882 0.1856 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 0.3878 313.676 283.186 0.612 0.982 0.320 11.894-9.307 99.02 97 4 0.1976 504.605 488.655 1.007 0.989 0.317 9.237-7.194 100.00 213 7 0.2204 412.667 402.197 1.061 0.993 0.293 7.162-5.571 100.00 427 22 0.2053 309.657 300.373 1.032 0.996 0.273 5.546-4.326 100.00 867 58 0.0988 425.114 420.170 1.074 0.999 0.250 4.315-3.360 100.00 1859 96 0.0556 404.288 404.541 1.150 1.002 0.228 3.356-3.002 100.00 1373 60 0.0414 311.400 311.421 1.133 1.006 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.6939 ================= 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 : 0.3627 0.2034 0.083 5.357 8.8 119.3 19.9 258 0.000 1_bss: 0.1556 0.1578 0.083 5.357 6.4 116.9 17.5 258 0.000 1_settarget: 0.1556 0.1578 0.083 5.357 6.4 116.9 17.5 258 0.000 1_nqh: 0.1556 0.1578 0.083 5.357 6.4 116.9 17.5 258 0.000 1_weight: 0.1556 0.1578 0.083 5.357 6.4 116.9 17.5 258 0.000 1_xyzrec: 0.1158 0.1785 0.009 0.968 6.4 116.9 17.5 258 0.211 1_adp: 0.1024 0.1782 0.009 0.968 2.3 111.9 17.8 258 0.211 1_regHadp: 0.1018 0.1785 0.009 0.968 2.3 111.9 17.8 258 0.211 1_occ: 0.1014 0.1780 0.009 0.968 2.3 111.9 17.8 258 0.211 2_bss: 0.1012 0.1782 0.009 0.968 1.2 110.8 16.7 258 0.211 2_settarget: 0.1012 0.1782 0.009 0.968 1.2 110.8 16.7 258 0.211 2_updatecdl: 0.1012 0.1782 0.009 0.999 1.2 110.8 16.7 258 0.211 2_nqh: 0.1012 0.1782 0.009 0.999 1.2 110.8 16.7 258 0.211 2_sol: 0.1113 0.1649 0.009 0.999 1.0 110.5 16.0 235 n/a 2_weight: 0.1113 0.1649 0.009 0.999 1.0 110.5 16.0 235 n/a 2_xyzrec: 0.1008 0.1789 0.009 0.952 1.0 110.5 16.0 235 n/a 2_adp: 0.0941 0.1828 0.009 0.952 0.0 107.5 16.6 235 n/a 2_regHadp: 0.0938 0.1830 0.009 0.952 0.0 107.5 16.6 235 n/a 2_occ: 0.0935 0.1816 0.009 0.952 0.0 107.5 16.6 235 n/a 3_bss: 0.0934 0.1825 0.009 0.952 0.0 107.5 16.6 235 n/a 3_settarget: 0.0934 0.1825 0.009 0.952 0.0 107.5 16.6 235 n/a 3_updatecdl: 0.0934 0.1825 0.009 0.958 0.0 107.5 16.6 235 n/a 3_nqh: 0.0935 0.1828 0.009 0.958 0.0 107.5 16.6 235 n/a 3_sol: 0.1049 0.1847 0.009 0.958 0.0 107.5 16.5 243 n/a 3_weight: 0.1049 0.1847 0.009 0.958 0.0 107.5 16.5 243 n/a 3_xyzrec: 0.0942 0.1835 0.011 1.043 0.0 107.5 16.5 243 n/a 3_adp: 0.0896 0.1839 0.011 1.043 0.0 108.1 16.5 243 n/a 3_regHadp: 0.0901 0.1843 0.011 1.043 0.0 108.1 16.5 243 n/a 3_occ: 0.0888 0.1816 0.011 1.043 0.0 108.1 16.5 243 n/a 4_bss: 0.0878 0.1804 0.011 1.043 0.0 108.1 16.5 243 n/a 4_settarget: 0.0878 0.1804 0.011 1.043 0.0 108.1 16.5 243 n/a 4_updatecdl: 0.0878 0.1804 0.011 1.051 0.0 108.1 16.5 243 n/a 4_nqh: 0.0878 0.1803 0.011 1.051 0.0 108.1 16.5 243 n/a 4_sol: 0.0995 0.1815 0.011 1.051 0.0 108.1 16.4 234 n/a 4_weight: 0.0995 0.1815 0.011 1.051 0.0 108.1 16.4 234 n/a 4_xyzrec: 0.0903 0.1878 0.011 1.036 0.0 108.1 16.4 234 n/a 4_adp: 0.0875 0.1896 0.011 1.036 0.0 105.8 16.7 234 n/a 4_regHadp: 0.0879 0.1896 0.011 1.036 0.0 105.8 16.7 234 n/a 4_occ: 0.0871 0.1883 0.011 1.036 0.0 105.8 16.7 234 n/a 5_bss: 0.0871 0.1877 0.011 1.036 0.0 105.8 16.7 234 n/a 5_settarget: 0.0871 0.1877 0.011 1.036 0.0 105.8 16.7 234 n/a 5_updatecdl: 0.0871 0.1877 0.011 1.039 0.0 105.8 16.7 234 n/a 5_setrh: 0.0874 0.1874 0.011 1.039 0.0 105.8 16.7 234 n/a 5_nqh: 0.0874 0.1874 0.011 1.039 0.0 105.8 16.7 234 n/a 5_sol: 0.0953 0.1862 0.011 1.039 0.0 105.8 16.7 228 n/a 5_weight: 0.0953 0.1862 0.011 1.039 0.0 105.8 16.7 228 n/a 5_xyzrec: 0.0901 0.1851 0.010 1.079 0.0 105.8 16.7 228 n/a 5_adp: 0.0885 0.1856 0.010 1.079 0.0 104.3 17.0 228 n/a 5_regHadp: 0.0889 0.1861 0.010 1.079 0.0 104.3 17.0 228 n/a 5_occ: 0.0883 0.1856 0.010 1.079 0.0 104.3 17.0 228 n/a end: 0.0882 0.1856 0.010 1.079 0.0 104.3 17.0 228 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2780949_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2780949_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1900 Refinement macro-cycles (run) : 487.8100 Write final files (write_after_run_outputs) : 10.6600 Total : 501.6600 Total CPU time: 8.68 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:02 PST -0800 (1735492742.72 s) Start R-work = 0.1556, R-free = 0.1578 Final R-work = 0.0882, R-free = 0.1856 =============================================================================== Job complete usr+sys time: 527.91 seconds wall clock time: 9 minutes 10.41 seconds (550.41 seconds total)