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_9394591.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9394591.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9394591.pdb" 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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.39, 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: 0.28 Conformation dependent library (CDL) restraints added in 106.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 541 0.92 - 1.18: 1132 1.18 - 1.45: 732 1.45 - 1.72: 732 1.72 - 1.99: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 1.459 1.692 -0.233 1.21e-02 6.83e+03 3.70e+02 bond pdb=" N THR A 140 " pdb=" CA THR A 140 " ideal model delta sigma weight residual 1.458 1.232 0.226 1.22e-02 6.72e+03 3.42e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.463 1.662 -0.198 1.08e-02 8.57e+03 3.37e+02 bond pdb=" C BGLU A 94 " pdb=" O BGLU A 94 " ideal model delta sigma weight residual 1.236 1.027 0.209 1.15e-02 7.56e+03 3.32e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.440 -0.206 1.19e-02 7.06e+03 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 3027 4.42 - 8.84: 1845 8.84 - 13.25: 728 13.25 - 17.67: 156 17.67 - 22.09: 21 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O AGLY A 65 " pdb=" C AGLY A 65 " pdb=" N APRO A 66 " ideal model delta sigma weight residual 121.77 137.63 -15.86 1.00e+00 1.00e+00 2.52e+02 angle pdb=" O VAL A 146 " pdb=" C VAL A 146 " pdb=" N GLU A 147 " ideal model delta sigma weight residual 123.05 139.49 -16.44 1.11e+00 8.12e-01 2.19e+02 angle pdb=" O THR A 160 " pdb=" C THR A 160 " pdb=" N SER A 161 " ideal model delta sigma weight residual 122.34 140.17 -17.83 1.25e+00 6.40e-01 2.04e+02 angle pdb=" O ALA A 167 " pdb=" C ALA A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.12 137.16 -15.04 1.06e+00 8.90e-01 2.01e+02 angle pdb=" O ASN A 173 " pdb=" C ASN A 173 " pdb=" N GLY A 174 " ideal model delta sigma weight residual 122.35 139.54 -17.19 1.23e+00 6.61e-01 1.95e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 21.29: 1359 21.29 - 42.57: 84 42.57 - 63.85: 33 63.85 - 85.13: 4 85.13 - 106.41: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 156 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " ideal model delta harmonic sigma weight residual -122.60 -147.50 24.90 0 2.50e+00 1.60e-01 9.92e+01 dihedral pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " ideal model delta harmonic sigma weight residual 122.80 145.52 -22.72 0 2.50e+00 1.60e-01 8.26e+01 dihedral pdb=" C GLU A 143 " pdb=" N GLU A 143 " pdb=" CA GLU A 143 " pdb=" CB GLU A 143 " ideal model delta harmonic sigma weight residual -122.60 -141.58 18.98 0 2.50e+00 1.60e-01 5.77e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.319: 137 0.319 - 0.631: 79 0.631 - 0.943: 21 0.943 - 1.255: 5 1.255 - 1.568: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.02 -1.57 2.00e-01 2.50e+01 6.14e+01 chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.06e+01 chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.98e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.158 9.50e-02 1.11e+02 9.57e-02 1.46e+02 pdb=" NE ARG A 48 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.133 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.089 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.088 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " 0.065 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.081 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " 0.096 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.012 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG TYR A 139 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.101 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.107 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.022 2.00e-02 2.50e+03 6.36e-02 9.11e+01 pdb=" CG HIS A 126 " 0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.104 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.102 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.042 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.043 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.057 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 526 2.23 - 2.82: 7384 2.82 - 3.41: 10808 3.41 - 4.01: 15431 4.01 - 4.60: 22530 Nonbonded interactions: 56679 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.633 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.816 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.819 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.839 2.450 nonbonded pdb=" O PRO A 22 " pdb=" H MET A 26 " model vdw 1.853 2.450 ... (remaining 56674 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_9394591_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= 0.3623 r_free= 0.2044 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.466553 | | target function (ml) not normalized (work): 22020.104010 | | target function (ml) not normalized (free): 1152.150598 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3824 0.2257 4.8525 4.9258| | 2: 3.78 - 3.00 1.00 2430 110 0.3379 0.1685 4.0695 4.1153| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 6607.18| | 2: 3.78 - 3.00 2430 110 0.94 11.39 1.48 0.26 450.54| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 381.68 max = 12063.22 mean = 3572.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.34| |phase err.(test): min = 0.00 max = 89.93 mean = 33.32| |-----------------------------------------------------------------------------| ----------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 0.235 1557 Z= 5.484 Angle : 5.353 19.110 2118 Z= 3.755 Chirality : 0.409 1.568 243 Planarity : 0.030 0.106 284 Dihedral : 14.604 106.413 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 2.48 % Favored : 95.03 % Cbeta Deviations : 31.89 % 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: -3.09 (0.46), residues: 224 helix: -2.93 (0.38), residues: 102 sheet: -0.89 (0.76), residues: 38 loop : -1.07 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.082 0.019 ARG A 145 TYR 0.100 0.043 TYR A 139 PHE 0.112 0.044 PHE A 119 HIS 0.099 0.041 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3623 r_free= 0.2044 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.466553 | | target function (ml) not normalized (work): 22020.104010 | | target function (ml) not normalized (free): 1152.150598 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3578 0.3655 0.2133 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3578 0.3655 0.2133 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2549 0.2133 n_refl.: 5178 overall B=-2.76 to atoms: r(all,work,free)=0.2420 0.2441 0.2086 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1563 0.1560 0.1612 n_refl.: 5178 remove outliers: r(all,work,free)=0.1558 0.1555 0.1612 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 0.3947 449.615 407.512 0.642 1.102 0.410 11.894-9.307 99.02 97 4 0.1899 714.250 694.594 0.906 1.096 0.403 9.237-7.194 100.00 213 7 0.2150 584.115 574.724 0.945 1.085 0.354 7.162-5.571 100.00 427 22 0.2289 438.307 423.703 0.914 1.066 0.304 5.546-4.326 100.00 867 58 0.1383 601.733 594.657 0.970 1.036 0.230 4.315-3.360 100.00 1859 96 0.1302 572.255 566.068 1.058 0.984 0.200 3.356-3.002 100.00 1373 60 0.1601 440.775 433.170 1.089 0.934 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.5252 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1612 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1557 r_free=0.1613 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.667053 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.869903 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 0.1159 0.1780 0.0621 0.009 1.0 3.5 0.5 0.0 0 9.334 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 17.80 6.21 3.013 16.101 1.870 0.018 10.21 17.93 7.72 4.829 16.270 1.870 0.014 Individual atomic B min max mean iso aniso Overall: 2.17 111.54 17.45 5.22 1785 0 Protein: 2.17 110.99 14.76 5.21 1519 0 Water: 4.11 111.54 33.11 N/A 258 0 Other: 16.31 37.55 23.78 N/A 8 0 Chain A: 2.17 111.54 17.45 N/A 1785 0 Histogram: Values Number of atoms 2.17 - 13.10 916 13.10 - 24.04 485 24.04 - 34.98 185 34.98 - 45.92 112 45.92 - 56.85 53 56.85 - 67.79 17 67.79 - 78.73 8 78.73 - 89.67 5 89.67 - 100.60 1 100.60 - 111.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1021 r_free=0.1793 r_work=0.1015 r_free=0.1799 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1015 r_free = 0.1799 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 = 0.1008 r_free = 0.1798 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1008 r_free= 0.1798 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013844 | | target function (ls_wunit_k1) not normalized (work): 68.167858 | | target function (ls_wunit_k1) not normalized (free): 10.566194 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1048 0.1008 0.1798 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2090 0.2090 0.2225 n_refl.: 5176 remove outliers: r(all,work,free)=0.2090 0.2090 0.2225 n_refl.: 5176 overall B=-0.92 to atoms: r(all,work,free)=0.2052 0.2049 0.2215 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1050 0.1010 0.1793 n_refl.: 5176 remove outliers: r(all,work,free)=0.1050 0.1010 0.1793 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 0.3337 329.354 312.686 0.667 1.033 0.388 11.894-9.307 99.02 97 4 0.1513 523.205 514.638 0.962 1.032 0.372 9.237-7.194 100.00 213 7 0.1632 427.878 428.085 0.999 1.029 0.331 7.162-5.571 100.00 427 22 0.1614 321.070 317.120 0.963 1.022 0.292 5.546-4.326 100.00 867 58 0.0900 440.784 437.985 0.987 1.012 0.202 4.315-3.360 100.00 1859 96 0.0764 419.190 419.100 1.045 0.994 0.193 3.356-3.002 100.00 1373 60 0.1013 322.878 321.388 1.031 0.976 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3058 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1010 r_free=0.1793 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1010 r_free=0.1793 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1793 | n_water=258 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.1033 r_free=0.1790 | n_water=249 | time (s): 23.780 (total time: 24.310) Filter (q & B) r_work=0.1034 r_free=0.1788 | n_water=246 | time (s): 1.990 (total time: 26.300) Compute maps r_work=0.1034 r_free=0.1788 | n_water=246 | time (s): 0.590 (total time: 26.890) Filter (map) r_work=0.1334 r_free=0.1833 | n_water=146 | time (s): 1.790 (total time: 28.680) Find peaks r_work=0.1334 r_free=0.1833 | n_water=146 | time (s): 0.400 (total time: 29.080) Add new water r_work=0.1692 r_free=0.2100 | n_water=231 | time (s): 1.220 (total time: 30.300) Refine new water occ: r_work=0.1169 r_free=0.1659 adp: r_work=0.1145 r_free=0.1664 occ: r_work=0.1144 r_free=0.1625 adp: r_work=0.1144 r_free=0.1625 occ: r_work=0.1144 r_free=0.1625 adp: r_work=0.1144 r_free=0.1625 ADP+occupancy (water only), MIN, final r_work=0.1144 r_free=0.1625 r_work=0.1144 r_free=0.1625 | n_water=231 | time (s): 5.680 (total time: 35.980) Filter (q & B) r_work=0.1145 r_free=0.1630 | n_water=230 | time (s): 1.460 (total time: 37.440) Filter (dist only) r_work=0.1156 r_free=0.1610 | n_water=225 | time (s): 18.850 (total time: 56.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.451728 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.876684 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 0.1030 0.1803 0.0774 0.009 1.0 4.2 0.5 0.6 0 11.226 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.30 18.03 7.74 4.624 16.641 2.877 0.014 9.58 18.65 9.07 5.536 16.941 2.877 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.28 16.06 6.54 1752 0 Protein: 0.00 107.28 14.79 6.52 1519 0 Water: 0.00 63.23 24.38 N/A 225 0 Other: 11.73 37.99 23.32 N/A 8 0 Chain A: 0.00 107.28 15.52 N/A 1669 0 Chain S: 6.63 47.15 26.91 N/A 83 0 Histogram: Values Number of atoms 0.00 - 10.73 722 10.73 - 21.46 641 21.46 - 32.19 208 32.19 - 42.91 115 42.91 - 53.64 32 53.64 - 64.37 18 64.37 - 75.10 9 75.10 - 85.83 3 85.83 - 96.56 2 96.56 - 107.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.0958 r_free=0.1865 r_work=0.0954 r_free=0.1867 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0954 r_free = 0.1867 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0955 r_free = 0.1868 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 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= 0.0955 r_free= 0.1868 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ls_wunit_k1) (work): 0.012484 | | target function (ls_wunit_k1) not normalized (work): 61.471212 | | target function (ls_wunit_k1) not normalized (free): 10.257751 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1000 0.0955 0.1868 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2118 0.2116 0.2295 n_refl.: 5176 remove outliers: r(all,work,free)=0.2118 0.2116 0.2295 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2118 0.2116 0.2295 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1001 0.0956 0.1867 n_refl.: 5176 remove outliers: r(all,work,free)=0.0999 0.0954 0.1867 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 0.3411 326.580 312.252 0.659 1.016 0.366 11.894-9.307 99.02 97 4 0.1514 523.205 515.259 0.966 1.017 0.363 9.237-7.194 100.00 213 7 0.1489 427.878 429.991 1.010 1.016 0.330 7.162-5.571 100.00 427 22 0.1438 321.070 318.501 0.988 1.013 0.300 5.546-4.326 100.00 867 58 0.0793 440.784 438.507 1.001 1.007 0.230 4.315-3.360 100.00 1859 96 0.0736 419.190 418.990 1.052 0.998 0.210 3.356-3.002 100.00 1373 60 0.0991 322.878 321.042 1.029 0.989 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-3.8641 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0954 r_free=0.1867 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0954 r_free=0.1867 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0954 r_free=0.1867 | n_water=225 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0974 r_free=0.1856 | n_water=221 | time (s): 20.160 (total time: 20.650) Filter (q & B) r_work=0.1060 r_free=0.1883 | n_water=218 | time (s): 1.430 (total time: 22.080) Compute maps r_work=0.1060 r_free=0.1883 | n_water=218 | time (s): 0.600 (total time: 22.680) Filter (map) r_work=0.1265 r_free=0.1884 | n_water=156 | time (s): 1.910 (total time: 24.590) Find peaks r_work=0.1265 r_free=0.1884 | n_water=156 | time (s): 0.610 (total time: 25.200) Add new water r_work=0.1654 r_free=0.2235 | n_water=236 | time (s): 1.660 (total time: 26.860) Refine new water occ: r_work=0.1072 r_free=0.1770 adp: r_work=0.1065 r_free=0.1772 occ: r_work=0.1051 r_free=0.1757 adp: r_work=0.1052 r_free=0.1763 occ: r_work=0.1039 r_free=0.1748 adp: r_work=0.1040 r_free=0.1751 ADP+occupancy (water only), MIN, final r_work=0.1040 r_free=0.1751 r_work=0.1040 r_free=0.1751 | n_water=236 | time (s): 8.210 (total time: 35.070) Filter (q & B) r_work=0.1040 r_free=0.1751 | n_water=236 | time (s): 1.050 (total time: 36.120) Filter (dist only) r_work=0.1051 r_free=0.1760 | n_water=233 | time (s): 18.690 (total time: 54.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.092826 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.210194 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 0.0946 0.1828 0.0883 0.011 1.0 4.8 0.5 0.0 0 0.546 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.46 18.28 8.83 5.444 17.583 0.210 5.159 9.01 18.11 9.10 7.200 17.556 0.210 5.058 Individual atomic B min max mean iso aniso Overall: 0.00 107.20 16.12 8.84 1760 0 Protein: 0.00 107.20 14.87 8.83 1519 0 Water: 0.00 58.23 24.01 N/A 233 0 Other: 12.94 42.96 24.57 N/A 8 0 Chain A: 0.00 107.20 15.52 N/A 1658 0 Chain S: 0.00 48.38 25.81 N/A 102 0 Histogram: Values Number of atoms 0.00 - 10.72 709 10.72 - 21.44 649 21.44 - 32.16 211 32.16 - 42.88 119 42.88 - 53.60 36 53.60 - 64.32 17 64.32 - 75.04 11 75.04 - 85.76 4 85.76 - 96.48 2 96.48 - 107.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1811 r_work=0.0907 r_free=0.1819 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0907 r_free = 0.1819 target_work(ml) = 5.060 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0890 r_free = 0.1799 target_work(ml) = 5.050 | | occupancies: max = 1.00 min = 0.24 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= 0.0890 r_free= 0.1799 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.050273 | | target function (ml) not normalized (work): 24862.495696 | | target function (ml) not normalized (free): 1807.671467 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0936 0.0890 0.1799 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2101 0.2113 0.2038 n_refl.: 5175 remove outliers: r(all,work,free)=0.2101 0.2113 0.2038 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2101 0.2113 0.2038 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0926 0.0880 0.1800 n_refl.: 5175 remove outliers: r(all,work,free)=0.0924 0.0878 0.1800 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3638 328.752 298.545 0.613 0.997 0.350 11.894-9.307 99.02 97 4 0.1713 523.205 511.091 0.948 1.001 0.350 9.237-7.194 100.00 213 7 0.1825 427.878 423.170 0.986 1.003 0.320 7.162-5.571 100.00 427 22 0.1804 321.070 311.572 0.971 1.003 0.290 5.546-4.326 100.00 867 58 0.0908 440.784 436.368 0.989 1.003 0.250 4.315-3.360 100.00 1859 96 0.0591 419.190 418.456 1.043 1.002 0.230 3.356-3.002 100.00 1373 60 0.0604 322.878 321.935 1.017 1.001 0.065 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-5.6607 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0878 r_free=0.1800 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B A 80 GLN B Total number of N/Q/H flips: 3 r_work=0.0883 r_free=0.1790 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0883 r_free=0.1790 | n_water=233 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.0901 r_free=0.1796 | n_water=227 | time (s): 19.280 (total time: 19.910) Filter (q & B) r_work=0.0970 r_free=0.1823 | n_water=225 | time (s): 1.680 (total time: 21.590) Compute maps r_work=0.0970 r_free=0.1823 | n_water=225 | time (s): 0.700 (total time: 22.290) Filter (map) r_work=0.1224 r_free=0.1853 | n_water=153 | time (s): 1.800 (total time: 24.090) Find peaks r_work=0.1224 r_free=0.1853 | n_water=153 | time (s): 0.430 (total time: 24.520) Add new water r_work=0.1552 r_free=0.2185 | n_water=230 | time (s): 1.650 (total time: 26.170) Refine new water occ: r_work=0.1005 r_free=0.1774 adp: r_work=0.0997 r_free=0.1785 occ: r_work=0.0990 r_free=0.1760 adp: r_work=0.0990 r_free=0.1772 occ: r_work=0.0983 r_free=0.1747 adp: r_work=0.0983 r_free=0.1759 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1759 r_work=0.0983 r_free=0.1759 | n_water=230 | time (s): 16.070 (total time: 42.240) Filter (q & B) r_work=0.0984 r_free=0.1767 | n_water=227 | time (s): 1.250 (total time: 43.490) Filter (dist only) r_work=0.0996 r_free=0.1762 | n_water=225 | time (s): 17.870 (total time: 61.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.003474 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.251666 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 0.0897 0.1865 0.0968 0.011 1.0 4.5 0.5 0.6 0 0.502 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.97 18.65 9.68 6.894 17.593 0.252 5.045 8.72 18.86 10.13 8.057 17.710 0.252 4.976 Individual atomic B min max mean iso aniso Overall: 0.00 107.10 16.31 10.51 1752 0 Protein: 0.00 107.10 15.26 10.51 1519 0 Water: 0.00 55.74 23.03 N/A 225 0 Other: 16.48 46.49 26.35 N/A 8 0 Chain A: 0.00 107.10 15.76 N/A 1645 0 Chain S: 0.00 55.74 24.63 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.71 698 10.71 - 21.42 617 21.42 - 32.13 258 32.13 - 42.84 105 42.84 - 53.55 38 53.55 - 64.26 18 64.26 - 74.97 6 74.97 - 85.68 7 85.68 - 96.39 3 96.39 - 107.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.0872 r_free=0.1886 r_work=0.0877 r_free=0.1892 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0877 r_free = 0.1892 target_work(ml) = 4.980 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0867 r_free = 0.1882 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0867 r_free= 0.1882 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 4.972582 | | target function (ml) not normalized (work): 24475.048437 | | target function (ml) not normalized (free): 2080.903730 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0918 0.0867 0.1882 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2092 0.2099 0.2122 n_refl.: 5174 remove outliers: r(all,work,free)=0.2092 0.2099 0.2122 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2092 0.2099 0.2122 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0916 0.0866 0.1884 n_refl.: 5174 remove outliers: r(all,work,free)=0.0916 0.0866 0.1884 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 0.3702 328.752 302.973 0.603 0.988 0.330 11.894-9.307 99.02 97 4 0.1751 523.205 511.223 0.949 0.994 0.330 9.237-7.194 100.00 213 7 0.2001 427.878 421.194 0.994 0.997 0.314 7.162-5.571 100.00 427 22 0.1948 321.070 310.328 0.984 0.998 0.300 5.546-4.326 100.00 867 58 0.0965 440.784 435.366 1.004 1.000 0.244 4.315-3.360 100.00 1859 96 0.0562 419.190 419.044 1.066 1.003 0.230 3.356-3.002 100.00 1373 60 0.0466 322.878 322.505 1.038 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.7836 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0866 r_free=0.1884 After: r_work=0.0869 r_free=0.1883 ================================== NQH flips ================================== r_work=0.0869 r_free=0.1883 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0869 r_free=0.1884 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0869 r_free=0.1884 | n_water=225 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0886 r_free=0.1903 | n_water=220 | time (s): 17.610 (total time: 18.180) Filter (q & B) r_work=0.0991 r_free=0.1936 | n_water=216 | time (s): 1.950 (total time: 20.130) Compute maps r_work=0.0991 r_free=0.1936 | n_water=216 | time (s): 0.670 (total time: 20.800) Filter (map) r_work=0.1245 r_free=0.2005 | n_water=146 | time (s): 1.590 (total time: 22.390) Find peaks r_work=0.1245 r_free=0.2005 | n_water=146 | time (s): 0.590 (total time: 22.980) Add new water r_work=0.1556 r_free=0.2307 | n_water=217 | time (s): 1.580 (total time: 24.560) Refine new water occ: r_work=0.1006 r_free=0.1941 adp: r_work=0.0999 r_free=0.1947 occ: r_work=0.0993 r_free=0.1923 adp: r_work=0.0992 r_free=0.1937 occ: r_work=0.0986 r_free=0.1911 adp: r_work=0.0985 r_free=0.1926 ADP+occupancy (water only), MIN, final r_work=0.0985 r_free=0.1926 r_work=0.0985 r_free=0.1926 | n_water=217 | time (s): 9.270 (total time: 33.830) Filter (q & B) r_work=0.0985 r_free=0.1933 | n_water=214 | time (s): 1.230 (total time: 35.060) Filter (dist only) r_work=0.0991 r_free=0.1940 | n_water=213 | time (s): 17.000 (total time: 52.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.018257 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.240001 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 0.0913 0.1946 0.1033 0.010 1.1 6.7 0.5 0.0 0 0.509 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.13 19.46 10.33 8.007 17.935 0.240 5.033 8.94 19.77 10.82 8.755 18.038 0.240 4.978 Individual atomic B min max mean iso aniso Overall: 0.00 107.38 16.50 11.51 1740 0 Protein: 0.00 107.38 15.59 11.51 1519 0 Water: 0.00 67.09 22.59 N/A 213 0 Other: 15.40 45.66 27.31 N/A 8 0 Chain A: 0.00 107.38 16.00 N/A 1633 0 Chain S: 0.00 67.09 24.21 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.74 674 10.74 - 21.48 621 21.48 - 32.21 251 32.21 - 42.95 115 42.95 - 53.69 39 53.69 - 64.43 19 64.43 - 75.17 8 75.17 - 85.90 8 85.90 - 96.64 3 96.64 - 107.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.0894 r_free=0.1977 r_work=0.0898 r_free=0.1977 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1977 target_work(ml) = 4.983 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0890 r_free = 0.1965 target_work(ml) = 4.977 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0890 r_free= 0.1965 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.977003 | | target function (ml) not normalized (work): 24496.807113 | | target function (ml) not normalized (free): 2167.979095 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1244 0.1967 5.5203 6.3171| | 2: 3.78 - 3.00 1.00 2430 110 0.0458 0.1962 4.4198 11.554| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.64 1.00 0.98 12154.06| | 2: 3.78 - 3.00 2430 110 0.99 2.08 1.00 1.00 1009.21| |alpha: min = 0.97 max = 1.01 mean = 0.99| |beta: min = 660.87 max = 20050.81 mean = 6651.83| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.15 mean = 6.92| |phase err.(test): min = 0.00 max = 83.61 mean = 7.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0943 0.0890 0.1965 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2155 0.2156 0.2271 n_refl.: 5174 remove outliers: r(all,work,free)=0.2155 0.2156 0.2271 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2155 0.2156 0.2271 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0940 0.0888 0.1956 n_refl.: 5174 remove outliers: r(all,work,free)=0.0940 0.0888 0.1956 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 0.3772 328.752 300.721 0.609 0.982 0.329 11.894-9.307 99.02 97 4 0.1788 523.205 510.424 0.968 0.990 0.329 9.237-7.194 100.00 213 7 0.2047 427.878 419.128 1.002 0.994 0.320 7.162-5.571 100.00 427 22 0.1996 321.070 311.417 0.983 0.996 0.269 5.546-4.326 100.00 867 58 0.1036 440.784 435.001 1.014 0.999 0.250 4.315-3.360 100.00 1859 96 0.0576 419.190 418.924 1.085 1.003 0.230 3.356-3.002 100.00 1373 60 0.0442 322.878 322.603 1.061 1.006 0.066 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6800 ================= 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 : 0.3623 0.2044 0.083 5.353 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1612 0.083 5.353 6.1 116.5 17.1 258 0.000 1_settarget: 0.1555 0.1612 0.083 5.353 6.1 116.5 17.1 258 0.000 1_nqh: 0.1557 0.1613 0.083 5.353 6.1 116.5 17.1 258 0.006 1_weight: 0.1557 0.1613 0.083 5.353 6.1 116.5 17.1 258 0.006 1_xyzrec: 0.1159 0.1780 0.009 0.961 6.1 116.5 17.1 258 0.216 1_adp: 0.1021 0.1793 0.009 0.961 2.2 111.5 17.4 258 0.216 1_regHadp: 0.1015 0.1799 0.009 0.961 2.2 111.5 17.4 258 0.216 1_occ: 0.1008 0.1798 0.009 0.961 2.2 111.5 17.4 258 0.216 2_bss: 0.1010 0.1793 0.009 0.961 1.2 110.6 16.5 258 0.216 2_settarget: 0.1010 0.1793 0.009 0.961 1.2 110.6 16.5 258 0.216 2_updatecdl: 0.1010 0.1793 0.009 0.980 1.2 110.6 16.5 258 0.216 2_nqh: 0.1010 0.1793 0.009 0.980 1.2 110.6 16.5 258 0.216 2_sol: 0.1156 0.1610 0.009 0.980 1.2 110.1 15.5 225 n/a 2_weight: 0.1156 0.1610 0.009 0.980 1.2 110.1 15.5 225 n/a 2_xyzrec: 0.1030 0.1803 0.009 0.973 1.2 110.1 15.5 225 n/a 2_adp: 0.0958 0.1865 0.009 0.973 0.0 107.3 16.1 225 n/a 2_regHadp: 0.0954 0.1867 0.009 0.973 0.0 107.3 16.1 225 n/a 2_occ: 0.0955 0.1868 0.009 0.973 0.0 107.3 16.1 225 n/a 3_bss: 0.0954 0.1867 0.009 0.973 0.0 107.3 16.1 225 n/a 3_settarget: 0.0954 0.1867 0.009 0.973 0.0 107.3 16.1 225 n/a 3_updatecdl: 0.0954 0.1867 0.009 0.981 0.0 107.3 16.1 225 n/a 3_nqh: 0.0954 0.1867 0.009 0.981 0.0 107.3 16.1 225 n/a 3_sol: 0.1051 0.1760 0.009 0.981 0.0 107.3 16.2 233 n/a 3_weight: 0.1051 0.1760 0.009 0.981 0.0 107.3 16.2 233 n/a 3_xyzrec: 0.0946 0.1828 0.011 1.039 0.0 107.3 16.2 233 n/a 3_adp: 0.0901 0.1811 0.011 1.039 0.0 107.2 16.1 233 n/a 3_regHadp: 0.0907 0.1819 0.011 1.039 0.0 107.2 16.1 233 n/a 3_occ: 0.0890 0.1799 0.011 1.039 0.0 107.2 16.1 233 n/a 4_bss: 0.0878 0.1800 0.011 1.039 0.0 107.2 16.1 233 n/a 4_settarget: 0.0878 0.1800 0.011 1.039 0.0 107.2 16.1 233 n/a 4_updatecdl: 0.0878 0.1800 0.011 1.040 0.0 107.2 16.1 233 n/a 4_nqh: 0.0883 0.1790 0.011 1.040 0.0 107.2 16.1 233 n/a 4_sol: 0.0996 0.1762 0.011 1.040 0.0 107.2 16.1 225 n/a 4_weight: 0.0996 0.1762 0.011 1.040 0.0 107.2 16.1 225 n/a 4_xyzrec: 0.0897 0.1865 0.011 1.041 0.0 107.2 16.1 225 n/a 4_adp: 0.0872 0.1886 0.011 1.041 0.0 107.1 16.3 225 n/a 4_regHadp: 0.0877 0.1892 0.011 1.041 0.0 107.1 16.3 225 n/a 4_occ: 0.0867 0.1882 0.011 1.041 0.0 107.1 16.3 225 n/a 5_bss: 0.0866 0.1884 0.011 1.041 0.0 107.1 16.3 225 n/a 5_settarget: 0.0866 0.1884 0.011 1.041 0.0 107.1 16.3 225 n/a 5_updatecdl: 0.0866 0.1884 0.011 1.051 0.0 107.1 16.3 225 n/a 5_setrh: 0.0869 0.1883 0.011 1.051 0.0 107.1 16.3 225 n/a 5_nqh: 0.0869 0.1884 0.011 1.051 0.0 107.1 16.3 225 n/a 5_sol: 0.0991 0.1940 0.011 1.051 0.0 107.1 16.3 213 n/a 5_weight: 0.0991 0.1940 0.011 1.051 0.0 107.1 16.3 213 n/a 5_xyzrec: 0.0913 0.1946 0.010 1.113 0.0 107.1 16.3 213 n/a 5_adp: 0.0894 0.1977 0.010 1.113 0.0 107.4 16.5 213 n/a 5_regHadp: 0.0898 0.1977 0.010 1.113 0.0 107.4 16.5 213 n/a 5_occ: 0.0890 0.1965 0.010 1.113 0.0 107.4 16.5 213 n/a end: 0.0888 0.1956 0.010 1.113 0.0 107.4 16.5 213 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9394591_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9394591_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.3600 Refinement macro-cycles (run) : 493.2300 Write final files (write_after_run_outputs) : 9.5900 Total : 507.1800 Total CPU time: 8.79 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:09 PST -0800 (1735492749.14 s) Start R-work = 0.1555, R-free = 0.1612 Final R-work = 0.0888, R-free = 0.1956 =============================================================================== Job complete usr+sys time: 534.82 seconds wall clock time: 9 minutes 17.42 seconds (557.42 seconds total)