Starting phenix.refine on Sun Dec 29 09:24:42 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=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9394591.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9394591.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.61, per 1000 atoms: 0.48 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: 0.41 Conformation dependent library (CDL) restraints added in 110.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2789 r_free= 0.1867 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406156 | | target function (ml) not normalized (work): 71569.196161 | | target function (ml) not normalized (free): 3290.587588 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3213 0.2192 7.4716 5.0459| | 2: 3.63 - 2.88 1.00 2711 122 0.2623 0.1688 4.3343 4.3207| | 3: 2.88 - 2.52 1.00 2682 148 0.2566 0.1785 4.1938 4.2033| | 4: 2.52 - 2.29 1.00 2661 139 0.2540 0.1737 3.5019 3.7089| | 5: 2.29 - 2.13 1.00 2678 122 0.2666 0.1508 3.4329 3.5013| | 6: 2.13 - 2.00 1.00 2692 117 0.2735 0.1815 3.3421 3.3878| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.88 0.77 0.23 1322.86| | 2: 3.63 - 2.88 2711 122 0.82 24.05 1.31 0.23 1322.86| | 3: 2.88 - 2.52 2682 148 0.73 33.15 1.28 0.23 1322.86| | 4: 2.52 - 2.29 2661 139 0.93 12.38 1.29 0.25 154.99| | 5: 2.29 - 2.13 2678 122 0.91 14.75 1.32 0.25 154.99| | 6: 2.13 - 2.00 2692 117 0.89 17.85 1.33 0.25 154.99| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 154.99 max = 1322.86 mean = 745.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 20.01| |phase err.(test): min = 0.00 max = 87.37 mean = 20.23| |-----------------------------------------------------------------------------| ----------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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2789 r_free= 0.1867 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406156 | | target function (ml) not normalized (work): 71569.196161 | | target function (ml) not normalized (free): 3290.587588 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2817 percent. r_work = 0.2918 r_free = 0.2005 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2864 0.2918 0.2005 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2864 0.2918 0.2005 n_refl.: 17050 remove outliers: r(all,work,free)=0.2153 0.2163 0.2005 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2128 0.2137 0.1987 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1612 0.1608 0.1681 n_refl.: 17045 remove outliers: r(all,work,free)=0.1610 0.1606 0.1681 n_refl.: 17043 ======================== 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 0.3946 399.041 360.164 0.646 1.019 0.402 11.894-9.307 99.02 97 4 0.1891 633.772 615.691 0.918 1.019 0.389 9.237-7.194 100.00 213 7 0.2149 518.362 509.277 0.954 1.018 0.350 7.162-5.571 100.00 427 22 0.2288 389.031 375.959 0.916 1.016 0.299 5.546-4.326 100.00 867 58 0.1393 534.077 528.614 0.959 1.013 0.235 4.315-3.360 100.00 1859 96 0.1288 507.912 503.759 1.015 1.008 0.211 3.356-2.611 100.00 3867 181 0.1666 333.670 328.984 1.010 0.998 0.071 2.608-2.000 99.99 8818 434 0.1630 217.495 213.874 1.036 0.982 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3950 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1606 r_free=0.1681 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=0.1607 r_free=0.1682 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.393726 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.916789 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1350 0.1636 0.0286 0.008 1.0 1.6 0.5 0.0 0 11.197 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.36 2.86 3.013 18.467 0.917 0.023 12.76 16.61 3.85 3.613 18.691 0.917 0.020 Individual atomic B min max mean iso aniso Overall: 5.92 113.91 19.92 4.11 1785 0 Protein: 5.92 113.16 17.15 4.11 1519 0 Water: 8.81 113.91 36.03 N/A 258 0 Other: 21.51 37.26 26.24 N/A 8 0 Chain A: 5.92 113.91 19.92 N/A 1785 0 Histogram: Values Number of atoms 5.92 - 16.72 1070 16.72 - 27.52 352 27.52 - 38.32 186 38.32 - 49.12 98 49.12 - 59.91 52 59.91 - 70.71 12 70.71 - 81.51 7 81.51 - 92.31 4 92.31 - 103.11 1 103.11 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1661 r_work=0.1279 r_free=0.1669 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1669 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1274 r_free = 0.1657 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1274 r_free= 0.1657 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019955 | | target function (ls_wunit_k1) not normalized (work): 323.988584 | | target function (ls_wunit_k1) not normalized (free): 27.458890 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1274 0.1657 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1898 0.1897 0.1984 n_refl.: 17043 remove outliers: r(all,work,free)=0.1898 0.1897 0.1984 n_refl.: 17043 overall B=-0.50 to atoms: r(all,work,free)=0.1862 0.1860 0.1963 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1291 0.1273 0.1646 n_refl.: 17043 remove outliers: r(all,work,free)=0.1290 0.1272 0.1646 n_refl.: 17042 ======================== 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 0.3557 304.639 282.784 0.642 1.006 0.380 11.894-9.307 99.02 97 4 0.1683 487.950 475.437 0.917 1.007 0.380 9.237-7.194 100.00 213 7 0.1800 399.094 395.707 0.959 1.007 0.351 7.162-5.571 100.00 427 22 0.1860 299.521 293.759 0.932 1.006 0.301 5.546-4.326 100.00 867 58 0.1048 411.194 408.447 0.959 1.005 0.221 4.315-3.360 100.00 1859 96 0.0926 391.049 390.338 1.015 1.004 0.192 3.356-2.611 100.00 3867 181 0.1296 256.897 255.560 1.008 1.001 0.091 2.608-2.000 99.99 8818 434 0.1345 167.453 166.094 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1418 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1646 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1274 r_free=0.1646 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1646 | n_water=258 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1282 r_free=0.1637 | n_water=252 | time (s): 20.950 (total time: 21.580) Filter (q & B) r_work=0.1281 r_free=0.1635 | n_water=250 | time (s): 1.630 (total time: 23.210) Compute maps r_work=0.1281 r_free=0.1635 | n_water=250 | time (s): 0.790 (total time: 24.000) Filter (map) r_work=0.1318 r_free=0.1644 | n_water=211 | time (s): 1.980 (total time: 25.980) Find peaks r_work=0.1318 r_free=0.1644 | n_water=211 | time (s): 0.480 (total time: 26.460) Add new water r_work=0.1542 r_free=0.1881 | n_water=358 | time (s): 1.620 (total time: 28.080) Refine new water occ: r_work=0.1341 r_free=0.1574 adp: r_work=0.1284 r_free=0.1578 occ: r_work=0.1288 r_free=0.1544 adp: r_work=0.1257 r_free=0.1560 occ: r_work=0.1257 r_free=0.1553 adp: r_work=0.1247 r_free=0.1558 ADP+occupancy (water only), MIN, final r_work=0.1247 r_free=0.1558 r_work=0.1247 r_free=0.1558 | n_water=358 | time (s): 12.210 (total time: 40.290) Filter (q & B) r_work=0.1248 r_free=0.1559 | n_water=354 | time (s): 2.180 (total time: 42.470) Filter (dist only) r_work=0.1248 r_free=0.1560 | n_water=352 | time (s): 29.900 (total time: 72.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.100652 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.988076 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1221 0.1611 0.0390 0.008 0.9 1.6 0.5 0.0 0 12.050 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 16.11 3.90 4.180 20.790 0.988 0.019 12.08 16.23 4.15 4.238 20.983 0.988 0.018 Individual atomic B min max mean iso aniso Overall: 6.41 107.66 20.88 4.19 1879 0 Protein: 6.41 107.66 17.41 4.18 1519 0 Water: 8.20 65.69 35.56 N/A 352 0 Other: 23.77 47.71 33.81 N/A 8 0 Chain A: 6.41 107.66 19.12 N/A 1738 0 Chain S: 17.20 62.59 42.57 N/A 141 0 Histogram: Values Number of atoms 6.41 - 16.54 1025 16.54 - 26.66 378 26.66 - 36.79 222 36.79 - 46.91 154 46.91 - 57.03 67 57.03 - 67.16 23 67.16 - 77.28 3 77.28 - 87.41 5 87.41 - 97.53 0 97.53 - 107.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1623 r_work=0.1210 r_free=0.1626 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1626 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1639 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1209 r_free= 0.1639 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017566 | | target function (ls_wunit_k1) not normalized (work): 285.181767 | | target function (ls_wunit_k1) not normalized (free): 26.168087 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1209 0.1639 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1798 0.1791 0.1986 n_refl.: 17042 remove outliers: r(all,work,free)=0.1798 0.1791 0.1986 n_refl.: 17042 overall B=-0.34 to atoms: r(all,work,free)=0.1776 0.1769 0.1971 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1205 0.1633 n_refl.: 17042 remove outliers: r(all,work,free)=0.1225 0.1204 0.1633 n_refl.: 17041 ======================== 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 0.3351 306.665 276.734 0.605 1.008 0.360 11.894-9.307 99.02 97 4 0.1520 487.950 485.302 0.921 1.008 0.360 9.237-7.194 100.00 213 7 0.1714 399.094 399.562 0.969 1.008 0.295 7.162-5.571 100.00 427 22 0.1658 299.521 295.078 0.936 1.007 0.271 5.546-4.326 100.00 867 58 0.0928 411.194 408.378 0.959 1.006 0.220 4.315-3.360 100.00 1859 96 0.0830 391.049 390.277 1.014 1.004 0.211 3.356-2.611 100.00 3867 181 0.1211 256.897 256.121 1.010 1.001 0.121 2.608-2.000 99.99 8818 434 0.1334 167.453 166.324 1.012 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1593 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1204 r_free=0.1633 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1204 r_free=0.1633 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1204 r_free=0.1633 | n_water=352 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.1204 r_free=0.1636 | n_water=349 | time (s): 27.800 (total time: 28.390) Filter (q & B) r_work=0.1204 r_free=0.1636 | n_water=349 | time (s): 0.760 (total time: 29.150) Compute maps r_work=0.1204 r_free=0.1636 | n_water=349 | time (s): 0.650 (total time: 29.800) Filter (map) r_work=0.1267 r_free=0.1638 | n_water=260 | time (s): 1.500 (total time: 31.300) Find peaks r_work=0.1267 r_free=0.1638 | n_water=260 | time (s): 0.480 (total time: 31.780) Add new water r_work=0.1452 r_free=0.1809 | n_water=408 | time (s): 1.360 (total time: 33.140) Refine new water occ: r_work=0.1258 r_free=0.1579 adp: r_work=0.1250 r_free=0.1583 occ: r_work=0.1232 r_free=0.1560 adp: r_work=0.1222 r_free=0.1561 occ: r_work=0.1215 r_free=0.1547 adp: r_work=0.1206 r_free=0.1550 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1550 r_work=0.1206 r_free=0.1550 | n_water=408 | time (s): 30.440 (total time: 63.580) Filter (q & B) r_work=0.1210 r_free=0.1557 | n_water=397 | time (s): 1.510 (total time: 65.090) Filter (dist only) r_work=0.1210 r_free=0.1557 | n_water=397 | time (s): 30.470 (total time: 95.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.824701 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.152885 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1187 0.1566 0.0379 0.009 0.9 4.8 0.5 0.0 0 0.912 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 15.66 3.79 4.256 21.163 0.153 5.003 11.70 15.77 4.08 4.827 21.086 0.153 4.982 Individual atomic B min max mean iso aniso Overall: 6.04 104.55 20.58 4.68 1924 0 Protein: 6.04 104.55 16.75 4.67 1519 0 Water: 8.22 60.35 34.95 N/A 397 0 Other: 26.59 43.88 34.54 N/A 8 0 Chain A: 6.04 104.55 18.47 N/A 1733 0 Chain S: 17.84 57.56 39.73 N/A 191 0 Histogram: Values Number of atoms 6.04 - 15.89 1058 15.89 - 25.74 349 25.74 - 35.59 232 35.59 - 45.44 162 45.44 - 55.29 88 55.29 - 65.14 21 65.14 - 75.00 5 75.00 - 84.85 5 84.85 - 94.70 2 94.70 - 104.55 2 =========================== Idealize ADP of riding H ========================== r_work=0.1170 r_free=0.1577 r_work=0.1170 r_free=0.1578 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1170 r_free = 0.1578 target_work(ml) = 4.982 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1165 r_free = 0.1580 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1165 r_free= 0.1580 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.978215 | | target function (ml) not normalized (work): 80816.339703 | | target function (ml) not normalized (free): 4199.058816 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1185 0.1165 0.1580 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1668 0.1659 0.1874 n_refl.: 17041 remove outliers: r(all,work,free)=0.1668 0.1659 0.1874 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1643 0.1634 0.1864 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1183 0.1163 0.1576 n_refl.: 17041 remove outliers: r(all,work,free)=0.1182 0.1162 0.1576 n_refl.: 17040 ======================== 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 93.75 85 5 0.3437 303.505 282.057 0.568 1.003 0.330 11.894-9.307 99.02 97 4 0.1794 487.950 480.341 0.914 1.004 0.330 9.237-7.194 100.00 213 7 0.1895 399.094 400.887 0.992 1.004 0.250 7.162-5.571 100.00 427 22 0.1709 299.521 293.991 0.946 1.004 0.241 5.546-4.326 100.00 867 58 0.0965 411.194 407.542 0.968 1.004 0.211 4.315-3.360 100.00 1859 96 0.0913 391.049 388.635 1.012 1.003 0.201 3.356-2.611 100.00 3867 181 0.1299 256.897 254.482 1.009 1.001 0.152 2.608-2.000 99.99 8818 434 0.1090 167.453 165.917 1.009 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1635 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1162 r_free=0.1576 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1164 r_free=0.1572 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1164 r_free=0.1572 | n_water=397 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1164 r_free=0.1572 | n_water=397 | time (s): 29.930 (total time: 30.600) Filter (q & B) r_work=0.1164 r_free=0.1573 | n_water=396 | time (s): 1.470 (total time: 32.070) Compute maps r_work=0.1164 r_free=0.1573 | n_water=396 | time (s): 0.540 (total time: 32.610) Filter (map) r_work=0.1212 r_free=0.1563 | n_water=310 | time (s): 2.020 (total time: 34.630) Find peaks r_work=0.1212 r_free=0.1563 | n_water=310 | time (s): 0.650 (total time: 35.280) Add new water r_work=0.1335 r_free=0.1674 | n_water=441 | time (s): 1.890 (total time: 37.170) Refine new water occ: r_work=0.1182 r_free=0.1519 adp: r_work=0.1174 r_free=0.1521 occ: r_work=0.1162 r_free=0.1507 adp: r_work=0.1153 r_free=0.1506 occ: r_work=0.1149 r_free=0.1502 adp: r_work=0.1142 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1142 r_free=0.1499 r_work=0.1142 r_free=0.1499 | n_water=441 | time (s): 40.050 (total time: 77.220) Filter (q & B) r_work=0.1146 r_free=0.1503 | n_water=428 | time (s): 2.060 (total time: 79.280) Filter (dist only) r_work=0.1146 r_free=0.1503 | n_water=428 | time (s): 32.840 (total time: 112.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.166134 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.186130 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1126 0.1557 0.0431 0.010 1.0 4.5 0.5 0.0 0 1.083 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.57 4.31 4.465 20.760 0.186 4.962 11.11 15.57 4.46 4.580 20.793 0.186 4.954 Individual atomic B min max mean iso aniso Overall: 5.49 102.95 20.67 4.91 1955 0 Protein: 5.49 102.95 16.38 4.90 1519 0 Water: 7.83 59.88 35.60 N/A 428 0 Other: 28.21 45.85 36.34 N/A 8 0 Chain A: 5.49 102.95 18.04 N/A 1732 0 Chain S: 19.77 59.88 41.07 N/A 223 0 Histogram: Values Number of atoms 5.49 - 15.24 1037 15.24 - 24.98 378 24.98 - 34.73 202 34.73 - 44.47 186 44.47 - 54.22 112 54.22 - 63.97 27 63.97 - 73.71 5 73.71 - 83.46 4 83.46 - 93.21 2 93.21 - 102.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1557 r_work=0.1111 r_free=0.1559 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1559 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1566 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1566 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.952448 | | target function (ml) not normalized (work): 80393.082527 | | target function (ml) not normalized (free): 4187.673940 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1102 0.1566 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1569 0.1556 0.1865 n_refl.: 17040 remove outliers: r(all,work,free)=0.1569 0.1556 0.1865 n_refl.: 17040 overall B=-0.25 to atoms: r(all,work,free)=0.1554 0.1540 0.1858 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1100 0.1563 n_refl.: 17040 remove outliers: r(all,work,free)=0.1121 0.1099 0.1563 n_refl.: 17039 ======================== 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 92.71 84 5 0.3430 299.937 283.056 0.561 1.003 0.340 11.894-9.307 99.02 97 4 0.1711 487.950 482.154 0.916 1.004 0.330 9.237-7.194 100.00 213 7 0.1776 399.094 400.065 0.988 1.004 0.240 7.162-5.571 100.00 427 22 0.1577 299.521 293.590 0.940 1.004 0.211 5.546-4.326 100.00 867 58 0.0911 411.194 407.920 0.963 1.004 0.187 4.315-3.360 100.00 1859 96 0.0844 391.049 388.522 1.004 1.003 0.178 3.356-2.611 100.00 3867 181 0.1220 256.897 254.634 1.001 1.001 0.151 2.608-2.000 99.99 8818 434 0.1048 167.453 166.255 0.996 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.8740 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1099 r_free=0.1563 After: r_work=0.1101 r_free=0.1562 ================================== NQH flips ================================== r_work=0.1101 r_free=0.1562 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1101 r_free=0.1562 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1101 r_free=0.1562 | n_water=428 | time (s): 0.790 (total time: 0.790) Filter (dist) r_work=0.1101 r_free=0.1562 | n_water=428 | time (s): 34.510 (total time: 35.300) Filter (q & B) r_work=0.1101 r_free=0.1562 | n_water=428 | time (s): 0.960 (total time: 36.260) Compute maps r_work=0.1101 r_free=0.1562 | n_water=428 | time (s): 0.810 (total time: 37.070) Filter (map) r_work=0.1166 r_free=0.1574 | n_water=336 | time (s): 2.300 (total time: 39.370) Find peaks r_work=0.1166 r_free=0.1574 | n_water=336 | time (s): 0.510 (total time: 39.880) Add new water r_work=0.1287 r_free=0.1701 | n_water=479 | time (s): 1.650 (total time: 41.530) Refine new water occ: r_work=0.1133 r_free=0.1516 adp: r_work=0.1127 r_free=0.1531 occ: r_work=0.1112 r_free=0.1495 adp: r_work=0.1105 r_free=0.1509 occ: r_work=0.1098 r_free=0.1482 adp: r_work=0.1092 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1092 r_free=0.1494 r_work=0.1092 r_free=0.1494 | n_water=479 | time (s): 22.750 (total time: 64.280) Filter (q & B) r_work=0.1097 r_free=0.1506 | n_water=466 | time (s): 1.690 (total time: 65.970) Filter (dist only) r_work=0.1097 r_free=0.1506 | n_water=466 | time (s): 38.130 (total time: 104.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.049018 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153791 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1116 0.1525 0.0409 0.011 1.1 5.4 0.5 0.0 0 1.025 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.25 4.09 4.577 20.763 0.154 4.944 11.07 15.09 4.02 4.678 20.770 0.154 4.935 Individual atomic B min max mean iso aniso Overall: 5.03 101.50 20.83 4.97 1993 0 Protein: 5.03 101.50 16.10 4.96 1519 0 Water: 7.69 66.43 36.05 N/A 466 0 Other: 26.84 43.21 34.45 N/A 8 0 Chain A: 5.03 101.50 17.74 N/A 1732 0 Chain S: 13.14 66.43 41.39 N/A 261 0 Histogram: Values Number of atoms 5.03 - 14.67 1000 14.67 - 24.32 407 24.32 - 33.97 207 33.97 - 43.62 208 43.62 - 53.26 114 53.26 - 62.91 35 62.91 - 72.56 12 72.56 - 82.20 4 82.20 - 91.85 2 91.85 - 101.50 4 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1509 r_work=0.1107 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1509 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1495 target_work(ml) = 4.927 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1099 r_free= 0.1495 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.927407 | | target function (ml) not normalized (work): 79981.678039 | | target function (ml) not normalized (free): 4159.078303 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2809 159 0.1113 0.1414 5.4417 5.6596| | 2: 3.63 - 2.88 1.00 2711 122 0.1069 0.1415 5.202 5.3331| | 3: 2.88 - 2.52 1.00 2681 148 0.1330 0.1659 5.1147 5.2008| | 4: 2.52 - 2.29 1.00 2661 139 0.0938 0.1511 4.6268 4.9455| | 5: 2.29 - 2.13 1.00 2678 122 0.0971 0.1461 4.5789 4.8723| | 6: 2.13 - 2.00 1.00 2692 117 0.1127 0.1705 4.5715 4.7607| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2809 159 0.95 8.88 1.00 0.96 6268.31| | 2: 3.63 - 2.88 2711 122 0.92 12.72 1.01 0.96 6268.31| | 3: 2.88 - 2.52 2681 148 0.88 18.84 0.99 0.96 6268.31| | 4: 2.52 - 2.29 2661 139 0.93 12.03 1.01 0.97 2098.92| | 5: 2.29 - 2.13 2678 122 0.91 14.08 1.00 0.97 2098.92| | 6: 2.13 - 2.00 2692 117 0.90 16.72 0.99 0.97 2098.92| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2098.92 max = 6268.31 mean = 4205.45| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.83 mean = 13.84| |phase err.(test): min = 0.00 max = 88.74 mean = 13.54| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1118 0.1099 0.1495 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1542 0.1528 0.1835 n_refl.: 17039 remove outliers: r(all,work,free)=0.1542 0.1528 0.1835 n_refl.: 17039 overall B=-0.20 to atoms: r(all,work,free)=0.1531 0.1516 0.1828 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1118 0.1099 0.1498 n_refl.: 17039 remove outliers: r(all,work,free)=0.1118 0.1099 0.1498 n_refl.: 17039 ======================== 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 92.71 84 5 0.3552 299.937 280.275 0.547 1.004 0.330 11.894-9.307 99.02 97 4 0.1746 487.950 483.451 0.911 1.005 0.330 9.237-7.194 100.00 213 7 0.1764 399.094 400.571 0.988 1.005 0.225 7.162-5.571 100.00 427 22 0.1535 299.521 293.448 0.936 1.005 0.220 5.546-4.326 100.00 867 58 0.0927 411.194 407.888 0.960 1.004 0.190 4.315-3.360 100.00 1859 96 0.0860 391.049 388.424 1.000 1.003 0.191 3.356-2.611 100.00 3867 181 0.1213 256.897 254.673 0.999 1.000 0.063 2.608-2.000 99.99 8818 434 0.1043 167.453 166.203 0.987 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.6878 ================= 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 : 0.2789 0.1867 0.083 5.353 8.8 119.3 19.9 258 0.000 1_bss: 0.1606 0.1681 0.083 5.353 8.5 118.9 19.5 258 0.000 1_settarget: 0.1606 0.1681 0.083 5.353 8.5 118.9 19.5 258 0.000 1_nqh: 0.1607 0.1682 0.083 5.353 8.5 118.9 19.5 258 0.006 1_weight: 0.1607 0.1682 0.083 5.353 8.5 118.9 19.5 258 0.006 1_xyzrec: 0.1350 0.1636 0.008 0.961 8.5 118.9 19.5 258 0.157 1_adp: 0.1276 0.1661 0.008 0.961 5.9 113.9 19.9 258 0.157 1_regHadp: 0.1279 0.1669 0.008 0.961 5.9 113.9 19.9 258 0.157 1_occ: 0.1274 0.1657 0.008 0.961 5.9 113.9 19.9 258 0.157 2_bss: 0.1272 0.1646 0.008 0.961 5.4 113.4 19.4 258 0.157 2_settarget: 0.1272 0.1646 0.008 0.961 5.4 113.4 19.4 258 0.157 2_updatecdl: 0.1272 0.1646 0.008 0.977 5.4 113.4 19.4 258 0.157 2_nqh: 0.1274 0.1646 0.008 0.977 5.4 113.4 19.4 258 0.154 2_sol: 0.1248 0.1560 0.008 0.977 5.4 112.7 20.5 352 n/a 2_weight: 0.1248 0.1560 0.008 0.977 5.4 112.7 20.5 352 n/a 2_xyzrec: 0.1221 0.1611 0.008 0.920 5.4 112.7 20.5 352 n/a 2_adp: 0.1208 0.1623 0.008 0.920 6.4 107.7 20.9 352 n/a 2_regHadp: 0.1210 0.1626 0.008 0.920 6.4 107.7 20.9 352 n/a 2_occ: 0.1209 0.1639 0.008 0.920 6.4 107.7 20.9 352 n/a 3_bss: 0.1204 0.1633 0.008 0.920 6.1 107.3 20.5 352 n/a 3_settarget: 0.1204 0.1633 0.008 0.920 6.1 107.3 20.5 352 n/a 3_updatecdl: 0.1204 0.1633 0.008 0.920 6.1 107.3 20.5 352 n/a 3_nqh: 0.1204 0.1633 0.008 0.920 6.1 107.3 20.5 352 n/a 3_sol: 0.1210 0.1557 0.008 0.920 6.1 107.3 20.7 397 n/a 3_weight: 0.1210 0.1557 0.008 0.920 6.1 107.3 20.7 397 n/a 3_xyzrec: 0.1187 0.1566 0.009 0.943 6.1 107.3 20.7 397 n/a 3_adp: 0.1170 0.1577 0.009 0.943 6.0 104.5 20.6 397 n/a 3_regHadp: 0.1170 0.1578 0.009 0.943 6.0 104.5 20.6 397 n/a 3_occ: 0.1165 0.1580 0.009 0.943 6.0 104.5 20.6 397 n/a 4_bss: 0.1162 0.1576 0.009 0.943 5.7 104.2 20.2 397 n/a 4_settarget: 0.1162 0.1576 0.009 0.943 5.7 104.2 20.2 397 n/a 4_updatecdl: 0.1162 0.1576 0.009 0.942 5.7 104.2 20.2 397 n/a 4_nqh: 0.1164 0.1572 0.009 0.942 5.7 104.2 20.2 397 n/a 4_sol: 0.1146 0.1503 0.009 0.942 5.7 104.2 20.6 428 n/a 4_weight: 0.1146 0.1503 0.009 0.942 5.7 104.2 20.6 428 n/a 4_xyzrec: 0.1126 0.1557 0.010 1.016 5.7 104.2 20.6 428 n/a 4_adp: 0.1111 0.1557 0.010 1.016 5.5 103.0 20.7 428 n/a 4_regHadp: 0.1111 0.1559 0.010 1.016 5.5 103.0 20.7 428 n/a 4_occ: 0.1102 0.1566 0.010 1.016 5.5 103.0 20.7 428 n/a 5_bss: 0.1099 0.1563 0.010 1.016 5.2 102.7 20.4 428 n/a 5_settarget: 0.1099 0.1563 0.010 1.016 5.2 102.7 20.4 428 n/a 5_updatecdl: 0.1099 0.1563 0.010 1.017 5.2 102.7 20.4 428 n/a 5_setrh: 0.1101 0.1562 0.010 1.017 5.2 102.7 20.4 428 n/a 5_nqh: 0.1101 0.1562 0.010 1.017 5.2 102.7 20.4 428 n/a 5_sol: 0.1097 0.1506 0.010 1.017 5.2 102.7 20.8 466 n/a 5_weight: 0.1097 0.1506 0.010 1.017 5.2 102.7 20.8 466 n/a 5_xyzrec: 0.1116 0.1525 0.011 1.062 5.2 102.7 20.8 466 n/a 5_adp: 0.1107 0.1509 0.011 1.062 5.0 101.5 20.8 466 n/a 5_regHadp: 0.1107 0.1509 0.011 1.062 5.0 101.5 20.8 466 n/a 5_occ: 0.1099 0.1495 0.011 1.062 5.0 101.5 20.8 466 n/a end: 0.1099 0.1498 0.011 1.062 4.8 101.3 20.6 466 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9394591_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9394591_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6900 Refinement macro-cycles (run) : 912.4900 Write final files (write_after_run_outputs) : 22.1100 Total : 938.2900 Total CPU time: 16.02 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:02 PST -0800 (1735494062.18 s) Start R-work = 0.1606, R-free = 0.1681 Final R-work = 0.1099, R-free = 0.1498 =============================================================================== Job complete usr+sys time: 984.94 seconds wall clock time: 16 minutes 47.74 seconds (1007.74 seconds total)