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_6847832.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_6847832.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6847832.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: 1.37, 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: 0.30 Conformation dependent library (CDL) restraints added in 135.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.61 - 0.89: 371 0.89 - 1.16: 1258 1.16 - 1.44: 696 1.44 - 1.71: 812 1.71 - 1.99: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.009 0.227 1.15e-02 7.56e+03 3.90e+02 bond pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 1.236 1.430 -0.194 9.90e-03 1.02e+04 3.86e+02 bond pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " ideal model delta sigma weight residual 1.326 1.535 -0.209 1.10e-02 8.26e+03 3.61e+02 bond pdb=" C ALA A 104 " pdb=" O ALA A 104 " ideal model delta sigma weight residual 1.234 1.014 0.220 1.18e-02 7.18e+03 3.47e+02 bond pdb=" C BLYS A 93 " pdb=" O BLYS A 93 " ideal model delta sigma weight residual 1.237 1.457 -0.221 1.19e-02 7.06e+03 3.43e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 3029 4.45 - 8.90: 1892 8.90 - 13.35: 700 13.35 - 17.80: 132 17.80 - 22.26: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 118 " pdb=" C GLY A 118 " pdb=" N PHE A 119 " ideal model delta sigma weight residual 122.54 107.69 14.85 1.02e+00 9.61e-01 2.12e+02 angle pdb=" O ALA A 79 " pdb=" C ALA A 79 " pdb=" N AGLN A 80 " ideal model delta sigma weight residual 122.07 136.61 -14.54 1.03e+00 9.43e-01 1.99e+02 angle pdb=" O BTYR A 67 " pdb=" C BTYR A 67 " pdb=" N ASP A 68 " ideal model delta sigma weight residual 123.24 107.34 15.90 1.23e+00 6.61e-01 1.67e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.80 107.28 14.52 1.13e+00 7.83e-01 1.65e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.60 -10.37 8.10e-01 1.52e+00 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 1309 17.65 - 35.29: 115 35.29 - 52.93: 45 52.93 - 70.58: 9 70.58 - 88.22: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C GLN A 95 " pdb=" N GLN A 95 " pdb=" CA GLN A 95 " pdb=" CB GLN A 95 " ideal model delta harmonic sigma weight residual -122.60 -144.23 21.63 0 2.50e+00 1.60e-01 7.48e+01 dihedral pdb=" N GLN A 95 " pdb=" C GLN A 95 " pdb=" CA GLN A 95 " pdb=" CB GLN A 95 " ideal model delta harmonic sigma weight residual 122.80 142.57 -19.77 0 2.50e+00 1.60e-01 6.26e+01 dihedral pdb=" N ARG A 27 " pdb=" C ARG A 27 " pdb=" CA ARG A 27 " pdb=" CB ARG A 27 " ideal model delta harmonic sigma weight residual 122.80 140.06 -17.26 0 2.50e+00 1.60e-01 4.77e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.227: 116 0.227 - 0.453: 75 0.453 - 0.678: 34 0.678 - 0.904: 14 0.904 - 1.129: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 3.56 -1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.53 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA GLN A 95 " pdb=" N GLN A 95 " pdb=" C GLN A 95 " pdb=" CB GLN A 95 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.135 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.112 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.070 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.026 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG TYR A 139 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.095 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.061 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.104 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.021 2.00e-02 2.50e+03 6.54e-02 1.28e+02 pdb=" CG TYR A 141 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.122 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.077 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.108 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.048 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.082 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 619 2.25 - 2.84: 7586 2.84 - 3.42: 10750 3.42 - 4.01: 15382 4.01 - 4.60: 22268 Nonbonded interactions: 56605 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.662 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.798 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.821 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.838 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.865 2.450 ... (remaining 56600 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_6847832_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= 0.3629 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469029 | | target function (ml) not normalized (work): 22032.314198 | | target function (ml) not normalized (free): 1142.979643 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3804 0.2180 4.8499 4.8888| | 2: 3.78 - 3.00 1.00 2430 110 0.3416 0.1614 4.0772 4.0797| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.76 0.83 0.13 6603.88| | 2: 3.78 - 3.00 2430 110 0.94 11.35 1.48 0.26 446.79| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 377.22 max = 12054.19 mean = 3569.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.32| |phase err.(test): min = 0.00 max = 90.00 mean = 33.53| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.227 1557 Z= 5.392 Angle : 5.351 17.239 2118 Z= 3.755 Chirality : 0.369 1.129 243 Planarity : 0.030 0.111 284 Dihedral : 14.223 88.220 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.32 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 29.73 % 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: -2.74 (0.47), residues: 224 helix: -3.19 (0.35), residues: 102 sheet: -0.39 (0.96), residues: 28 loop : -0.30 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.084 0.015 ARG A 98 TYR 0.099 0.044 TYR A 141 PHE 0.104 0.043 PHE A 119 HIS 0.067 0.025 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3629 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469029 | | target function (ml) not normalized (work): 22032.314198 | | target function (ml) not normalized (free): 1142.979643 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3582 0.3660 0.2090 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3582 0.3660 0.2090 n_refl.: 5182 remove outliers: r(all,work,free)=0.2527 0.2553 0.2090 n_refl.: 5178 overall B=-2.82 to atoms: r(all,work,free)=0.2419 0.2442 0.2043 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1560 0.1559 0.1583 n_refl.: 5178 remove outliers: r(all,work,free)=0.1556 0.1554 0.1583 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 0.3885 449.587 409.257 0.636 1.111 0.404 11.894-9.307 99.02 97 4 0.1877 714.205 689.586 0.906 1.104 0.387 9.237-7.194 100.00 213 7 0.2162 584.078 573.914 0.932 1.092 0.384 7.162-5.571 100.00 427 22 0.2286 438.279 424.305 0.913 1.071 0.326 5.546-4.326 100.00 867 58 0.1392 601.695 595.058 0.966 1.038 0.226 4.315-3.360 100.00 1859 96 0.1299 572.219 565.636 1.063 0.983 0.200 3.356-3.002 100.00 1373 60 0.1601 440.747 432.501 1.096 0.929 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6082 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1554 r_free=0.1583 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** A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1555 r_free=0.1582 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.721572 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.834116 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 0.1161 0.1786 0.0625 0.010 1.0 2.6 0.5 0.0 0 9.361 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 17.86 6.25 3.013 16.037 1.834 0.018 10.27 17.59 7.32 4.770 16.200 1.834 0.015 Individual atomic B min max mean iso aniso Overall: 2.08 111.48 17.37 5.16 1785 0 Protein: 2.08 111.15 14.68 5.15 1519 0 Water: 4.04 111.48 33.03 N/A 258 0 Other: 17.74 38.18 24.08 N/A 8 0 Chain A: 2.08 111.48 17.37 N/A 1785 0 Histogram: Values Number of atoms 2.08 - 13.02 927 13.02 - 23.96 474 23.96 - 34.90 189 34.90 - 45.84 107 45.84 - 56.78 58 56.78 - 67.72 13 67.72 - 78.66 8 78.66 - 89.60 5 89.60 - 100.54 1 100.54 - 111.48 3 =========================== Idealize ADP of riding H ========================== r_work=0.1027 r_free=0.1759 r_work=0.1020 r_free=0.1767 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1020 r_free = 0.1767 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 = 0.1019 r_free = 0.1771 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1019 r_free= 0.1771 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014160 | | target function (ls_wunit_k1) not normalized (work): 69.725967 | | target function (ls_wunit_k1) not normalized (free): 10.542408 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1057 0.1019 0.1771 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2093 0.2092 0.2219 n_refl.: 5176 remove outliers: r(all,work,free)=0.2093 0.2092 0.2219 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2053 0.2051 0.2208 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1062 0.1024 0.1768 n_refl.: 5176 remove outliers: r(all,work,free)=0.1062 0.1024 0.1768 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 0.3277 330.342 321.244 0.703 1.002 0.381 11.894-9.307 99.02 97 4 0.1521 524.775 517.615 0.993 1.004 0.361 9.237-7.194 100.00 213 7 0.1690 429.162 429.420 1.025 1.004 0.326 7.162-5.571 100.00 427 22 0.1648 322.034 317.886 0.981 1.003 0.312 5.546-4.326 100.00 867 58 0.0915 442.106 438.523 0.997 1.001 0.192 4.315-3.360 100.00 1859 96 0.0777 420.448 420.288 1.042 0.999 0.183 3.356-3.002 100.00 1373 60 0.1016 323.847 322.112 1.010 0.997 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3888 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1024 r_free=0.1768 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1026 r_free=0.1773 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1026 r_free=0.1773 | n_water=258 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1055 r_free=0.1764 | n_water=248 | time (s): 21.680 (total time: 22.300) Filter (q & B) r_work=0.1054 r_free=0.1766 | n_water=245 | time (s): 1.930 (total time: 24.230) Compute maps r_work=0.1054 r_free=0.1766 | n_water=245 | time (s): 0.570 (total time: 24.800) Filter (map) r_work=0.1371 r_free=0.1813 | n_water=141 | time (s): 1.840 (total time: 26.640) Find peaks r_work=0.1371 r_free=0.1813 | n_water=141 | time (s): 0.610 (total time: 27.250) Add new water r_work=0.1743 r_free=0.2048 | n_water=238 | time (s): 1.560 (total time: 28.810) Refine new water occ: r_work=0.1159 r_free=0.1698 adp: r_work=0.1135 r_free=0.1680 occ: r_work=0.1131 r_free=0.1683 adp: r_work=0.1119 r_free=0.1670 occ: r_work=0.1117 r_free=0.1670 adp: r_work=0.1114 r_free=0.1664 ADP+occupancy (water only), MIN, final r_work=0.1114 r_free=0.1664 r_work=0.1114 r_free=0.1664 | n_water=238 | time (s): 4.590 (total time: 33.400) Filter (q & B) r_work=0.1114 r_free=0.1665 | n_water=237 | time (s): 1.790 (total time: 35.190) Filter (dist only) r_work=0.1114 r_free=0.1662 | n_water=236 | time (s): 19.340 (total time: 54.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.594153 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.724238 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 0.1004 0.1796 0.0793 0.009 1.0 3.5 0.5 0.6 0 11.297 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.04 17.96 7.93 4.583 16.796 2.724 0.014 9.31 18.06 8.76 5.487 17.213 2.724 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.56 16.69 6.49 1763 0 Protein: 0.00 107.56 15.02 6.46 1519 0 Water: 0.00 62.81 26.96 N/A 236 0 Other: 18.73 48.71 31.19 N/A 8 0 Chain A: 0.00 107.56 15.79 N/A 1667 0 Chain S: 2.12 62.09 32.29 N/A 96 0 Histogram: Values Number of atoms 0.00 - 10.76 692 10.76 - 21.51 646 21.51 - 32.27 213 32.27 - 43.03 126 43.03 - 53.78 45 53.78 - 64.54 27 64.54 - 75.29 7 75.29 - 86.05 2 86.05 - 96.81 3 96.81 - 107.56 2 =========================== Idealize ADP of riding H ========================== r_work=0.0931 r_free=0.1806 r_work=0.0927 r_free=0.1805 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0927 r_free = 0.1805 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0924 r_free = 0.1814 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.21 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= 0.0924 r_free= 0.1814 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011716 | | target function (ls_wunit_k1) not normalized (work): 57.687747 | | target function (ls_wunit_k1) not normalized (free): 10.253949 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0970 0.0924 0.1814 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2112 0.2113 0.2251 n_refl.: 5176 remove outliers: r(all,work,free)=0.2112 0.2113 0.2251 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2112 0.2113 0.2251 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0968 0.0923 0.1816 n_refl.: 5176 remove outliers: r(all,work,free)=0.0967 0.0921 0.1816 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 0.3085 327.560 313.986 0.688 1.010 0.371 11.894-9.307 99.02 97 4 0.1465 524.775 518.222 0.975 1.012 0.340 9.237-7.194 100.00 213 7 0.1459 429.162 429.300 1.016 1.011 0.330 7.162-5.571 100.00 427 22 0.1390 322.034 318.911 0.990 1.008 0.290 5.546-4.326 100.00 867 58 0.0766 442.106 439.777 1.001 1.005 0.220 4.315-3.360 100.00 1859 96 0.0715 420.448 420.252 1.051 0.998 0.190 3.356-3.002 100.00 1373 60 0.0957 323.847 323.277 1.029 0.992 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.8988 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0921 r_free=0.1816 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0923 r_free=0.1818 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0923 r_free=0.1818 | n_water=236 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0951 r_free=0.1827 | n_water=228 | time (s): 17.230 (total time: 17.840) Filter (q & B) r_work=0.1007 r_free=0.1836 | n_water=226 | time (s): 1.420 (total time: 19.260) Compute maps r_work=0.1007 r_free=0.1836 | n_water=226 | time (s): 0.460 (total time: 19.720) Filter (map) r_work=0.1255 r_free=0.1825 | n_water=155 | time (s): 1.300 (total time: 21.020) Find peaks r_work=0.1255 r_free=0.1825 | n_water=155 | time (s): 0.560 (total time: 21.580) Add new water r_work=0.1630 r_free=0.2172 | n_water=237 | time (s): 1.380 (total time: 22.960) Refine new water occ: r_work=0.1063 r_free=0.1750 adp: r_work=0.1057 r_free=0.1758 occ: r_work=0.1045 r_free=0.1742 adp: r_work=0.1044 r_free=0.1749 occ: r_work=0.1034 r_free=0.1736 adp: r_work=0.1033 r_free=0.1740 ADP+occupancy (water only), MIN, final r_work=0.1033 r_free=0.1740 r_work=0.1033 r_free=0.1740 | n_water=237 | time (s): 8.990 (total time: 31.950) Filter (q & B) r_work=0.1034 r_free=0.1742 | n_water=235 | time (s): 1.840 (total time: 33.790) Filter (dist only) r_work=0.1045 r_free=0.1768 | n_water=233 | time (s): 18.740 (total time: 52.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.078878 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.237498 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 0.0938 0.1859 0.0921 0.010 1.0 3.5 0.5 0.6 0 0.539 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.38 18.59 9.21 5.427 17.869 0.237 5.158 8.96 19.08 10.12 7.130 17.863 0.237 5.063 Individual atomic B min max mean iso aniso Overall: 0.00 107.29 16.41 8.73 1760 0 Protein: 0.00 107.29 15.13 8.70 1519 0 Water: 0.00 57.81 24.18 N/A 233 0 Other: 14.95 53.92 32.00 N/A 8 0 Chain A: 0.00 107.29 15.81 N/A 1654 0 Chain S: 0.00 55.61 25.75 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.73 677 10.73 - 21.46 667 21.46 - 32.19 228 32.19 - 42.92 112 42.92 - 53.64 39 53.64 - 64.37 19 64.37 - 75.10 11 75.10 - 85.83 2 85.83 - 96.56 3 96.56 - 107.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.0896 r_free=0.1908 r_work=0.0902 r_free=0.1918 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0902 r_free = 0.1918 target_work(ml) = 5.067 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0893 r_free = 0.1904 target_work(ml) = 5.061 | | occupancies: max = 1.00 min = 0.20 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= 0.0893 r_free= 0.1904 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.060768 | | target function (ml) not normalized (work): 24914.159324 | | target function (ml) not normalized (free): 1886.296067 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0945 0.0893 0.1904 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2126 0.2131 0.2184 n_refl.: 5175 remove outliers: r(all,work,free)=0.2126 0.2131 0.2184 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2126 0.2131 0.2184 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0937 0.0886 0.1915 n_refl.: 5175 remove outliers: r(all,work,free)=0.0937 0.0886 0.1915 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 0.3679 327.560 299.030 0.644 0.996 0.371 11.894-9.307 99.02 97 4 0.1824 524.775 509.935 0.946 0.999 0.335 9.237-7.194 100.00 213 7 0.1868 429.162 423.786 0.993 1.000 0.304 7.162-5.571 100.00 427 22 0.1819 322.034 312.291 0.970 1.000 0.290 5.546-4.326 100.00 867 58 0.0906 442.106 437.585 0.990 1.001 0.240 4.315-3.360 100.00 1859 96 0.0588 420.448 419.566 1.044 1.001 0.207 3.356-3.002 100.00 1373 60 0.0616 323.847 322.722 1.022 1.001 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-5.7840 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0886 r_free=0.1915 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.0886 r_free=0.1916 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0886 r_free=0.1916 | n_water=233 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0902 r_free=0.1939 | n_water=229 | time (s): 17.090 (total time: 17.660) Filter (q & B) r_work=0.0959 r_free=0.1963 | n_water=226 | time (s): 1.290 (total time: 18.950) Compute maps r_work=0.0959 r_free=0.1963 | n_water=226 | time (s): 0.540 (total time: 19.490) Filter (map) r_work=0.1210 r_free=0.1966 | n_water=155 | time (s): 1.880 (total time: 21.370) Find peaks r_work=0.1210 r_free=0.1966 | n_water=155 | time (s): 0.600 (total time: 21.970) Add new water r_work=0.1589 r_free=0.2281 | n_water=239 | time (s): 1.840 (total time: 23.810) Refine new water occ: r_work=0.1036 r_free=0.1915 adp: r_work=0.1034 r_free=0.1932 occ: r_work=0.1020 r_free=0.1899 adp: r_work=0.1021 r_free=0.1918 occ: r_work=0.1007 r_free=0.1885 adp: r_work=0.1008 r_free=0.1901 ADP+occupancy (water only), MIN, final r_work=0.1008 r_free=0.1901 r_work=0.1008 r_free=0.1901 | n_water=239 | time (s): 12.700 (total time: 36.510) Filter (q & B) r_work=0.1008 r_free=0.1901 | n_water=239 | time (s): 1.190 (total time: 37.700) Filter (dist only) r_work=0.1007 r_free=0.1908 | n_water=237 | time (s): 18.240 (total time: 55.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.020254 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.254102 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 0.0909 0.1959 0.1050 0.010 1.0 3.2 0.5 0.6 0 0.510 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.09 19.59 10.50 6.834 18.033 0.254 5.042 8.88 19.54 10.66 8.067 18.096 0.254 4.980 Individual atomic B min max mean iso aniso Overall: 0.00 107.87 16.68 10.43 1764 0 Protein: 0.00 107.87 15.46 10.40 1519 0 Water: 0.00 58.58 23.94 N/A 237 0 Other: 16.79 56.30 32.70 N/A 8 0 Chain A: 0.00 107.87 15.99 N/A 1641 0 Chain S: 0.00 58.58 25.76 N/A 123 0 Histogram: Values Number of atoms 0.00 - 10.79 669 10.79 - 21.57 651 21.57 - 32.36 250 32.36 - 43.15 112 43.15 - 53.94 42 53.94 - 64.72 22 64.72 - 75.51 8 75.51 - 86.30 5 86.30 - 97.09 4 97.09 - 107.87 1 =========================== Idealize ADP of riding H ========================== r_work=0.0888 r_free=0.1954 r_work=0.0892 r_free=0.1959 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0892 r_free = 0.1959 target_work(ml) = 4.985 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0877 r_free = 0.1949 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0877 r_free= 0.1949 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.972939 | | target function (ml) not normalized (work): 24481.780431 | | target function (ml) not normalized (free): 2139.818402 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0932 0.0877 0.1949 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2164 0.2167 0.2263 n_refl.: 5175 remove outliers: r(all,work,free)=0.2164 0.2167 0.2263 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2164 0.2167 0.2263 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0929 0.0876 0.1938 n_refl.: 5175 remove outliers: r(all,work,free)=0.0927 0.0873 0.1938 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 0.3794 329.738 284.920 0.579 0.991 0.330 11.894-9.307 99.02 97 4 0.1926 524.775 513.529 0.963 0.995 0.330 9.237-7.194 100.00 213 7 0.2078 429.162 418.167 1.010 0.997 0.310 7.162-5.571 100.00 427 22 0.1960 322.034 311.859 0.992 0.998 0.300 5.546-4.326 100.00 867 58 0.0967 442.106 436.111 1.009 1.000 0.224 4.315-3.360 100.00 1859 96 0.0552 420.448 419.918 1.075 1.002 0.210 3.356-3.002 100.00 1373 60 0.0466 323.847 323.463 1.055 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-7.3150 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0873 r_free=0.1938 After: r_work=0.0876 r_free=0.1937 ================================== NQH flips ================================== r_work=0.0876 r_free=0.1937 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.0877 r_free=0.1934 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0877 r_free=0.1934 | n_water=237 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0901 r_free=0.1943 | n_water=231 | time (s): 19.100 (total time: 19.570) Filter (q & B) r_work=0.1004 r_free=0.1955 | n_water=228 | time (s): 1.280 (total time: 20.850) Compute maps r_work=0.1004 r_free=0.1955 | n_water=228 | time (s): 0.450 (total time: 21.300) Filter (map) r_work=0.1274 r_free=0.1997 | n_water=153 | time (s): 1.540 (total time: 22.840) Find peaks r_work=0.1274 r_free=0.1997 | n_water=153 | time (s): 0.460 (total time: 23.300) Add new water r_work=0.1570 r_free=0.2276 | n_water=221 | time (s): 1.280 (total time: 24.580) Refine new water occ: r_work=0.1015 r_free=0.1896 adp: r_work=0.1005 r_free=0.1908 occ: r_work=0.0997 r_free=0.1897 adp: r_work=0.0996 r_free=0.1905 occ: r_work=0.0989 r_free=0.1894 adp: r_work=0.0988 r_free=0.1901 ADP+occupancy (water only), MIN, final r_work=0.0988 r_free=0.1901 r_work=0.0988 r_free=0.1901 | n_water=221 | time (s): 11.560 (total time: 36.140) Filter (q & B) r_work=0.0988 r_free=0.1901 | n_water=221 | time (s): 1.220 (total time: 37.360) Filter (dist only) r_work=0.0987 r_free=0.1904 | n_water=220 | time (s): 17.010 (total time: 54.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.952689 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.236603 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 0.0933 0.1909 0.0976 0.010 1.1 7.4 0.5 0.6 0 0.476 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.33 19.09 9.76 7.958 18.221 0.237 5.058 9.07 19.01 9.94 8.819 18.366 0.237 4.993 Individual atomic B min max mean iso aniso Overall: 0.00 107.18 16.87 11.63 1747 0 Protein: 0.00 107.18 15.93 11.59 1519 0 Water: 0.00 62.58 22.85 N/A 220 0 Other: 14.46 58.40 30.91 N/A 8 0 Chain A: 0.00 107.18 16.36 N/A 1629 0 Chain S: 0.00 62.58 23.87 N/A 118 0 Histogram: Values Number of atoms 0.00 - 10.72 646 10.72 - 21.44 637 21.44 - 32.15 268 32.15 - 42.87 112 42.87 - 53.59 44 53.59 - 64.31 21 64.31 - 75.02 8 75.02 - 85.74 4 85.74 - 96.46 5 96.46 - 107.18 2 =========================== Idealize ADP of riding H ========================== r_work=0.0907 r_free=0.1901 r_work=0.0911 r_free=0.1904 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0911 r_free = 0.1904 target_work(ml) = 4.999 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0904 r_free = 0.1898 target_work(ml) = 4.993 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0904 r_free= 0.1898 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.993095 | | target function (ml) not normalized (work): 24576.015058 | | target function (ml) not normalized (free): 2132.433949 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1267 0.1865 5.5426 6.27| | 2: 3.78 - 3.00 1.00 2430 110 0.0461 0.1955 4.4296 11.292| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.20 1.00 0.98 12998.46| | 2: 3.78 - 3.00 2430 110 0.99 2.09 1.00 1.00 1039.65| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 675.65 max = 21469.07 mean = 7094.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.95 mean = 7.21| |phase err.(test): min = 0.00 max = 75.35 mean = 7.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0954 0.0904 0.1898 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2161 0.2156 0.2355 n_refl.: 5174 remove outliers: r(all,work,free)=0.2161 0.2156 0.2355 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2161 0.2156 0.2355 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0954 0.0904 0.1902 n_refl.: 5174 remove outliers: r(all,work,free)=0.0954 0.0904 0.1902 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 0.3914 329.738 298.631 0.596 0.986 0.320 11.894-9.307 99.02 97 4 0.1898 524.775 508.441 0.963 0.992 0.323 9.237-7.194 100.00 213 7 0.2099 429.162 418.103 1.009 0.995 0.304 7.162-5.571 100.00 427 22 0.2031 322.034 311.310 0.991 0.997 0.287 5.546-4.326 100.00 867 58 0.1039 442.106 435.883 1.019 0.999 0.250 4.315-3.360 100.00 1859 96 0.0591 420.448 420.194 1.088 1.002 0.210 3.356-3.002 100.00 1373 60 0.0442 323.847 323.842 1.071 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9563 ================= 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 : 0.3629 0.1970 0.081 5.351 8.8 119.3 19.9 258 0.000 1_bss: 0.1554 0.1583 0.081 5.351 6.0 116.5 17.1 258 0.000 1_settarget: 0.1554 0.1583 0.081 5.351 6.0 116.5 17.1 258 0.000 1_nqh: 0.1555 0.1582 0.081 5.351 6.0 116.5 17.1 258 0.003 1_weight: 0.1555 0.1582 0.081 5.351 6.0 116.5 17.1 258 0.003 1_xyzrec: 0.1161 0.1786 0.010 0.960 6.0 116.5 17.1 258 0.212 1_adp: 0.1027 0.1759 0.010 0.960 2.1 111.5 17.4 258 0.212 1_regHadp: 0.1020 0.1767 0.010 0.960 2.1 111.5 17.4 258 0.212 1_occ: 0.1019 0.1771 0.010 0.960 2.1 111.5 17.4 258 0.212 2_bss: 0.1024 0.1768 0.010 0.960 1.1 110.5 16.4 258 0.212 2_settarget: 0.1024 0.1768 0.010 0.960 1.1 110.5 16.4 258 0.212 2_updatecdl: 0.1024 0.1768 0.010 0.985 1.1 110.5 16.4 258 0.212 2_nqh: 0.1026 0.1773 0.010 0.985 1.1 110.5 16.4 258 0.212 2_sol: 0.1114 0.1662 0.010 0.985 1.0 110.2 15.9 236 n/a 2_weight: 0.1114 0.1662 0.010 0.985 1.0 110.2 15.9 236 n/a 2_xyzrec: 0.1004 0.1796 0.009 0.957 1.0 110.2 15.9 236 n/a 2_adp: 0.0931 0.1806 0.009 0.957 0.0 107.6 16.7 236 n/a 2_regHadp: 0.0927 0.1805 0.009 0.957 0.0 107.6 16.7 236 n/a 2_occ: 0.0924 0.1814 0.009 0.957 0.0 107.6 16.7 236 n/a 3_bss: 0.0921 0.1816 0.009 0.957 0.0 107.6 16.7 236 n/a 3_settarget: 0.0921 0.1816 0.009 0.957 0.0 107.6 16.7 236 n/a 3_updatecdl: 0.0921 0.1816 0.009 0.959 0.0 107.6 16.7 236 n/a 3_nqh: 0.0923 0.1818 0.009 0.959 0.0 107.6 16.7 236 n/a 3_sol: 0.1045 0.1768 0.009 0.959 0.0 107.6 16.4 233 n/a 3_weight: 0.1045 0.1768 0.009 0.959 0.0 107.6 16.4 233 n/a 3_xyzrec: 0.0938 0.1859 0.010 1.025 0.0 107.6 16.4 233 n/a 3_adp: 0.0896 0.1908 0.010 1.025 0.0 107.3 16.4 233 n/a 3_regHadp: 0.0902 0.1918 0.010 1.025 0.0 107.3 16.4 233 n/a 3_occ: 0.0893 0.1904 0.010 1.025 0.0 107.3 16.4 233 n/a 4_bss: 0.0886 0.1915 0.010 1.025 0.0 107.3 16.4 233 n/a 4_settarget: 0.0886 0.1915 0.010 1.025 0.0 107.3 16.4 233 n/a 4_updatecdl: 0.0886 0.1915 0.010 1.036 0.0 107.3 16.4 233 n/a 4_nqh: 0.0886 0.1916 0.010 1.036 0.0 107.3 16.4 233 n/a 4_sol: 0.1007 0.1908 0.010 1.036 0.0 107.3 16.6 237 n/a 4_weight: 0.1007 0.1908 0.010 1.036 0.0 107.3 16.6 237 n/a 4_xyzrec: 0.0909 0.1959 0.010 1.021 0.0 107.3 16.6 237 n/a 4_adp: 0.0888 0.1954 0.010 1.021 0.0 107.9 16.7 237 n/a 4_regHadp: 0.0892 0.1959 0.010 1.021 0.0 107.9 16.7 237 n/a 4_occ: 0.0877 0.1949 0.010 1.021 0.0 107.9 16.7 237 n/a 5_bss: 0.0873 0.1938 0.010 1.021 0.0 107.9 16.7 237 n/a 5_settarget: 0.0873 0.1938 0.010 1.021 0.0 107.9 16.7 237 n/a 5_updatecdl: 0.0873 0.1938 0.010 1.031 0.0 107.9 16.7 237 n/a 5_setrh: 0.0876 0.1937 0.010 1.031 0.0 107.9 16.7 237 n/a 5_nqh: 0.0877 0.1934 0.010 1.031 0.0 107.9 16.7 237 n/a 5_sol: 0.0987 0.1904 0.010 1.031 0.0 107.9 16.6 220 n/a 5_weight: 0.0987 0.1904 0.010 1.031 0.0 107.9 16.6 220 n/a 5_xyzrec: 0.0933 0.1909 0.010 1.101 0.0 107.9 16.6 220 n/a 5_adp: 0.0907 0.1901 0.010 1.101 0.0 107.2 16.9 220 n/a 5_regHadp: 0.0911 0.1904 0.010 1.101 0.0 107.2 16.9 220 n/a 5_occ: 0.0904 0.1898 0.010 1.101 0.0 107.2 16.9 220 n/a end: 0.0904 0.1902 0.010 1.101 0.0 107.2 16.9 220 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6847832_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6847832_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1500 Refinement macro-cycles (run) : 492.6300 Write final files (write_after_run_outputs) : 9.5900 Total : 505.3700 Total CPU time: 8.77 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:08 PST -0800 (1735492748.16 s) Start R-work = 0.1554, R-free = 0.1583 Final R-work = 0.0904, R-free = 0.1902 =============================================================================== Job complete usr+sys time: 533.49 seconds wall clock time: 9 minutes 16.22 seconds (556.22 seconds total)