Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8315495.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_8315495.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8315495.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 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.25, per 1000 atoms: 0.37 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: 0.34 Conformation dependent library (CDL) restraints added in 119.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 547 0.91 - 1.17: 1097 1.17 - 1.42: 632 1.42 - 1.68: 839 1.68 - 1.94: 38 Bond restraints: 3153 Sorted by residual: bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.454 1.725 -0.271 1.18e-02 7.18e+03 5.28e+02 bond pdb=" CA GLU A 147 " pdb=" C GLU A 147 " ideal model delta sigma weight residual 1.522 1.277 0.246 1.19e-02 7.06e+03 4.27e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.545 -0.219 1.10e-02 8.26e+03 3.97e+02 bond pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 1.236 1.056 0.181 1.02e-02 9.61e+03 3.14e+02 bond pdb=" C SER A 57 " pdb=" O SER A 57 " ideal model delta sigma weight residual 1.234 1.447 -0.213 1.23e-02 6.61e+03 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3263 4.85 - 9.70: 1816 9.70 - 14.55: 612 14.55 - 19.40: 79 19.40 - 24.25: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 130.32 -9.90 6.40e-01 2.44e+00 2.39e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 120.55 105.90 14.65 9.50e-01 1.11e+00 2.38e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.12 107.07 15.05 1.06e+00 8.90e-01 2.02e+02 angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.77 135.47 -13.70 1.00e+00 1.00e+00 1.88e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 108.48 13.29 1.00e+00 1.00e+00 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 1315 17.65 - 35.30: 112 35.30 - 52.95: 40 52.95 - 70.61: 12 70.61 - 88.26: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C AGLU A 90 " pdb=" N AGLU A 90 " pdb=" CA AGLU A 90 " pdb=" CB AGLU A 90 " ideal model delta harmonic sigma weight residual -122.60 -142.47 19.87 0 2.50e+00 1.60e-01 6.32e+01 dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -142.17 19.57 0 2.50e+00 1.60e-01 6.13e+01 dihedral pdb=" N AGLU A 90 " pdb=" C AGLU A 90 " pdb=" CA AGLU A 90 " pdb=" CB AGLU A 90 " ideal model delta harmonic sigma weight residual 122.80 141.69 -18.89 0 2.50e+00 1.60e-01 5.71e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 105 0.216 - 0.431: 72 0.431 - 0.646: 41 0.646 - 0.862: 22 0.862 - 1.077: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA AGLU A 64 " pdb=" N AGLU A 64 " pdb=" C AGLU A 64 " pdb=" CB AGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 3.39 -0.88 2.00e-01 2.50e+01 1.94e+01 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 3.32 -0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.100 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.014 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.067 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.023 2.00e-02 2.50e+03 6.25e-02 1.17e+02 pdb=" CG PHE A 119 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.088 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.125 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.085 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.078 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.011 9.50e-02 1.11e+02 6.69e-02 1.00e+02 pdb=" NE ARG A 28 " -0.106 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " 0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.082 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " -0.071 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.078 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1025 2.31 - 2.88: 8054 2.88 - 3.46: 10574 3.46 - 4.03: 15124 4.03 - 4.60: 21875 Nonbonded interactions: 56652 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.741 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.743 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.770 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.787 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.788 2.100 ... (remaining 56647 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_8315495_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= 0.3620 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467508 | | target function (ml) not normalized (work): 22024.816788 | | target function (ml) not normalized (free): 1146.228261 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3802 0.2214 4.8508 4.9174| | 2: 3.78 - 3.00 1.00 2430 110 0.3397 0.1627 4.0732 4.0723| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.90 0.83 0.13 6613.29| | 2: 3.78 - 3.00 2430 110 0.94 11.36 1.48 0.26 451.60| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 383.96 max = 12079.26 mean = 3576.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.40| |phase err.(test): min = 0.00 max = 89.96 mean = 33.19| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.271 1557 Z= 5.557 Angle : 5.380 22.608 2118 Z= 3.810 Chirality : 0.381 1.077 243 Planarity : 0.033 0.126 284 Dihedral : 13.949 88.257 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 24.86 % 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: -1.85 (0.47), residues: 224 helix: -2.24 (0.40), residues: 102 sheet: -0.68 (0.82), residues: 28 loop : 0.15 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.018 ARG A 28 TYR 0.116 0.041 TYR A 141 PHE 0.113 0.040 PHE A 119 HIS 0.067 0.033 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= 0.3620 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467508 | | target function (ml) not normalized (work): 22024.816788 | | target function (ml) not normalized (free): 1146.228261 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3575 0.3653 0.2096 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3575 0.3653 0.2096 n_refl.: 5182 remove outliers: r(all,work,free)=0.2529 0.2554 0.2096 n_refl.: 5178 overall B=-2.84 to atoms: r(all,work,free)=0.2419 0.2441 0.2046 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1556 0.1557 0.1547 n_refl.: 5178 remove outliers: r(all,work,free)=0.1552 0.1552 0.1547 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 0.3869 449.839 409.334 0.646 1.093 0.406 11.894-9.307 99.02 97 4 0.1862 714.605 695.116 0.915 1.088 0.382 9.237-7.194 100.00 213 7 0.2177 584.405 576.763 0.956 1.079 0.371 7.162-5.571 100.00 427 22 0.2332 438.525 426.030 0.921 1.062 0.346 5.546-4.326 100.00 867 58 0.1392 602.033 594.650 0.971 1.033 0.267 4.315-3.360 100.00 1859 96 0.1298 572.539 566.382 1.056 0.986 0.200 3.356-3.002 100.00 1373 60 0.1579 440.994 433.913 1.088 0.939 0.107 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6342 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1552 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1552 r_free=0.1547 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.609129 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.985314 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 0.1171 0.1787 0.0616 0.010 1.0 2.6 0.5 0.0 0 9.805 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.71 17.87 6.16 3.013 16.017 1.985 0.018 10.29 17.91 7.62 4.972 16.194 1.985 0.015 Individual atomic B min max mean iso aniso Overall: 2.24 111.69 17.38 5.37 1785 0 Protein: 2.24 111.69 14.69 5.37 1519 0 Water: 4.02 111.46 33.00 N/A 258 0 Other: 17.50 36.55 23.80 N/A 8 0 Chain A: 2.24 111.69 17.38 N/A 1785 0 Histogram: Values Number of atoms 2.24 - 13.18 911 13.18 - 24.13 493 24.13 - 35.08 190 35.08 - 46.02 105 46.02 - 56.97 55 56.97 - 67.91 15 67.91 - 78.86 7 78.86 - 89.80 5 89.80 - 100.75 1 100.75 - 111.69 3 =========================== Idealize ADP of riding H ========================== r_work=0.1029 r_free=0.1791 r_work=0.1023 r_free=0.1799 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1023 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 = 0.1019 r_free = 0.1788 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 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= 0.1019 r_free= 0.1788 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.014139 | | target function (ls_wunit_k1) not normalized (work): 69.619267 | | target function (ls_wunit_k1) not normalized (free): 10.568113 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1058 0.1019 0.1788 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2106 0.2106 0.2219 n_refl.: 5176 remove outliers: r(all,work,free)=0.2106 0.2106 0.2219 n_refl.: 5176 overall B=-0.93 to atoms: r(all,work,free)=0.2067 0.2065 0.2208 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1019 0.1774 n_refl.: 5176 remove outliers: r(all,work,free)=0.1058 0.1019 0.1774 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 0.3261 330.198 312.229 0.663 1.032 0.381 11.894-9.307 99.02 97 4 0.1522 524.546 517.593 0.963 1.032 0.356 9.237-7.194 100.00 213 7 0.1665 428.974 428.557 1.005 1.028 0.336 7.162-5.571 100.00 427 22 0.1638 321.893 318.183 0.963 1.022 0.322 5.546-4.326 100.00 867 58 0.0922 441.913 438.604 0.989 1.011 0.242 4.315-3.360 100.00 1859 96 0.0775 420.264 420.166 1.044 0.993 0.193 3.356-3.002 100.00 1373 60 0.1001 323.705 322.016 1.034 0.975 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3451 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1019 r_free=0.1774 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1019 r_free=0.1773 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1773 | n_water=258 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.1040 r_free=0.1759 | n_water=249 | time (s): 19.980 (total time: 20.520) Filter (q & B) r_work=0.1039 r_free=0.1761 | n_water=246 | time (s): 1.870 (total time: 22.390) Compute maps r_work=0.1039 r_free=0.1761 | n_water=246 | time (s): 0.620 (total time: 23.010) Filter (map) r_work=0.1355 r_free=0.1802 | n_water=140 | time (s): 1.440 (total time: 24.450) Find peaks r_work=0.1355 r_free=0.1802 | n_water=140 | time (s): 0.420 (total time: 24.870) Add new water r_work=0.1723 r_free=0.2059 | n_water=227 | time (s): 1.210 (total time: 26.080) Refine new water occ: r_work=0.1171 r_free=0.1650 adp: r_work=0.1147 r_free=0.1662 occ: r_work=0.1143 r_free=0.1634 adp: r_work=0.1133 r_free=0.1639 occ: r_work=0.1132 r_free=0.1628 adp: r_work=0.1129 r_free=0.1630 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1630 r_work=0.1129 r_free=0.1630 | n_water=227 | time (s): 4.550 (total time: 30.630) Filter (q & B) r_work=0.1129 r_free=0.1630 | n_water=227 | time (s): 0.890 (total time: 31.520) Filter (dist only) r_work=0.1135 r_free=0.1639 | n_water=224 | time (s): 18.210 (total time: 49.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.891011 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.751620 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 0.1012 0.1808 0.0796 0.009 1.0 3.8 0.5 0.6 0 11.446 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.12 18.08 7.96 4.708 16.780 2.752 0.014 9.45 18.29 8.84 5.462 17.161 2.752 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.84 16.55 6.37 1751 0 Protein: 0.00 106.84 15.00 6.34 1519 0 Water: 0.00 62.81 26.62 N/A 224 0 Other: 16.11 44.57 28.12 N/A 8 0 Chain A: 0.00 106.84 15.69 N/A 1664 0 Chain S: 0.32 60.20 32.86 N/A 87 0 Histogram: Values Number of atoms 0.00 - 10.68 675 10.68 - 21.37 676 21.37 - 32.05 196 32.05 - 42.74 125 42.74 - 53.42 39 53.42 - 64.10 25 64.10 - 74.79 8 74.79 - 85.47 2 85.47 - 96.16 3 96.16 - 106.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.0945 r_free=0.1829 r_work=0.0943 r_free=0.1828 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0943 r_free = 0.1828 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0940 r_free = 0.1820 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.22 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= 0.0940 r_free= 0.1820 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012082 | | target function (ls_wunit_k1) not normalized (work): 59.490154 | | target function (ls_wunit_k1) not normalized (free): 9.998745 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0984 0.0940 0.1820 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2160 0.2163 0.2233 n_refl.: 5176 remove outliers: r(all,work,free)=0.2160 0.2163 0.2233 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2160 0.2163 0.2233 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0986 0.0942 0.1837 n_refl.: 5176 remove outliers: r(all,work,free)=0.0986 0.0942 0.1837 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 0.3118 330.198 314.688 0.676 1.039 0.381 11.894-9.307 99.02 97 4 0.1443 524.546 518.433 0.948 1.038 0.345 9.237-7.194 100.00 213 7 0.1472 428.974 430.338 0.992 1.034 0.325 7.162-5.571 100.00 427 22 0.1395 321.893 320.489 0.967 1.027 0.320 5.546-4.326 100.00 867 58 0.0799 441.913 439.539 0.991 1.014 0.260 4.315-3.360 100.00 1859 96 0.0734 420.264 419.714 1.052 0.993 0.196 3.356-3.002 100.00 1373 60 0.0979 323.705 322.294 1.047 0.972 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.7256 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0942 r_free=0.1837 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 3 r_work=0.0943 r_free=0.1840 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0943 r_free=0.1840 | n_water=224 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0945 r_free=0.1821 | n_water=222 | time (s): 18.180 (total time: 18.790) Filter (q & B) r_work=0.1067 r_free=0.1822 | n_water=217 | time (s): 1.560 (total time: 20.350) Compute maps r_work=0.1067 r_free=0.1822 | n_water=217 | time (s): 0.540 (total time: 20.890) Filter (map) r_work=0.1316 r_free=0.1915 | n_water=145 | time (s): 1.660 (total time: 22.550) Find peaks r_work=0.1316 r_free=0.1915 | n_water=145 | time (s): 0.470 (total time: 23.020) Add new water r_work=0.1666 r_free=0.2230 | n_water=230 | time (s): 1.360 (total time: 24.380) Refine new water occ: r_work=0.1058 r_free=0.1808 adp: r_work=0.1045 r_free=0.1827 occ: r_work=0.1034 r_free=0.1810 adp: r_work=0.1034 r_free=0.1817 occ: r_work=0.1025 r_free=0.1801 adp: r_work=0.1024 r_free=0.1805 ADP+occupancy (water only), MIN, final r_work=0.1024 r_free=0.1805 r_work=0.1024 r_free=0.1805 | n_water=230 | time (s): 11.180 (total time: 35.560) Filter (q & B) r_work=0.1025 r_free=0.1808 | n_water=229 | time (s): 1.460 (total time: 37.020) Filter (dist only) r_work=0.1042 r_free=0.1823 | n_water=227 | time (s): 16.330 (total time: 53.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.172084 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.232856 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 0.0937 0.1838 0.0901 0.011 1.1 4.8 0.5 0.6 0 0.586 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.37 18.38 9.01 5.347 17.801 0.233 5.164 8.96 18.53 9.57 7.070 17.790 0.233 5.072 Individual atomic B min max mean iso aniso Overall: 0.00 106.99 16.36 8.69 1754 0 Protein: 0.00 106.99 15.07 8.66 1519 0 Water: 0.00 69.56 24.51 N/A 227 0 Other: 16.20 46.24 29.58 N/A 8 0 Chain A: 0.00 106.99 15.74 N/A 1648 0 Chain S: 0.00 69.56 26.00 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.70 687 10.70 - 21.40 646 21.40 - 32.10 233 32.10 - 42.80 113 42.80 - 53.50 39 53.50 - 64.20 17 64.20 - 74.90 11 74.90 - 85.59 3 85.59 - 96.29 4 96.29 - 106.99 1 =========================== Idealize ADP of riding H ========================== r_work=0.0896 r_free=0.1853 r_work=0.0902 r_free=0.1861 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0902 r_free = 0.1861 target_work(ml) = 5.076 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0889 r_free = 0.1841 target_work(ml) = 5.067 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0889 r_free= 0.1841 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.067390 | | target function (ml) not normalized (work): 24951.830215 | | target function (ml) not normalized (free): 1799.422147 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0937 0.0889 0.1841 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2154 0.2164 0.2128 n_refl.: 5176 remove outliers: r(all,work,free)=0.2154 0.2164 0.2128 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2154 0.2164 0.2128 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0933 0.0885 0.1847 n_refl.: 5176 remove outliers: r(all,work,free)=0.0931 0.0883 0.1847 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 0.3572 327.417 305.821 0.644 1.002 0.377 11.894-9.307 99.02 97 4 0.1853 524.546 511.572 0.939 1.006 0.340 9.237-7.194 100.00 213 7 0.1823 428.974 423.884 0.992 1.007 0.320 7.162-5.571 100.00 427 22 0.1731 321.893 315.384 0.961 1.006 0.320 5.546-4.326 100.00 867 58 0.0911 441.913 437.306 0.983 1.004 0.260 4.315-3.360 100.00 1859 96 0.0592 420.264 419.331 1.038 1.001 0.209 3.356-3.002 100.00 1373 60 0.0633 323.705 322.382 1.021 0.997 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-5.5257 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0883 r_free=0.1847 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0883 r_free=0.1847 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0883 r_free=0.1847 | n_water=227 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0890 r_free=0.1859 | n_water=225 | time (s): 16.790 (total time: 17.300) Filter (q & B) r_work=0.0935 r_free=0.1867 | n_water=222 | time (s): 1.510 (total time: 18.810) Compute maps r_work=0.0935 r_free=0.1867 | n_water=222 | time (s): 0.620 (total time: 19.430) Filter (map) r_work=0.1203 r_free=0.1964 | n_water=151 | time (s): 1.860 (total time: 21.290) Find peaks r_work=0.1203 r_free=0.1964 | n_water=151 | time (s): 0.530 (total time: 21.820) Add new water r_work=0.1517 r_free=0.2273 | n_water=222 | time (s): 1.510 (total time: 23.330) Refine new water occ: r_work=0.1004 r_free=0.1844 adp: r_work=0.1000 r_free=0.1856 occ: r_work=0.0992 r_free=0.1837 adp: r_work=0.0992 r_free=0.1849 occ: r_work=0.0984 r_free=0.1828 adp: r_work=0.0983 r_free=0.1840 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1840 r_work=0.0983 r_free=0.1840 | n_water=222 | time (s): 11.120 (total time: 34.450) Filter (q & B) r_work=0.0983 r_free=0.1840 | n_water=221 | time (s): 1.620 (total time: 36.070) Filter (dist only) r_work=0.0982 r_free=0.1844 | n_water=220 | time (s): 16.950 (total time: 53.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.984456 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.263802 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 0.0902 0.1883 0.0981 0.010 1.0 4.2 0.5 0.6 0 0.492 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.02 18.83 9.81 6.804 17.858 0.264 5.054 8.80 19.29 10.49 8.128 17.960 0.264 4.996 Individual atomic B min max mean iso aniso Overall: 0.00 106.68 16.51 10.60 1747 0 Protein: 0.00 106.68 15.43 10.58 1519 0 Water: 0.00 62.22 23.46 N/A 220 0 Other: 14.67 45.10 29.44 N/A 8 0 Chain A: 0.00 106.68 15.98 N/A 1639 0 Chain S: 0.00 62.22 24.58 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.67 661 10.67 - 21.34 651 21.34 - 32.00 238 32.00 - 42.67 123 42.67 - 53.34 37 53.34 - 64.01 15 64.01 - 74.67 10 74.67 - 85.34 8 85.34 - 96.01 3 96.01 - 106.68 1 =========================== Idealize ADP of riding H ========================== r_work=0.0880 r_free=0.1929 r_work=0.0884 r_free=0.1932 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0884 r_free = 0.1932 target_work(ml) = 5.002 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0869 r_free = 0.1919 target_work(ml) = 4.991 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0869 r_free= 0.1919 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.990680 | | target function (ml) not normalized (work): 24569.119808 | | target function (ml) not normalized (free): 2089.717935 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0922 0.0869 0.1919 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2212 0.2222 0.2187 n_refl.: 5175 remove outliers: r(all,work,free)=0.2212 0.2222 0.2187 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2212 0.2222 0.2187 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0920 0.0868 0.1927 n_refl.: 5175 remove outliers: r(all,work,free)=0.0920 0.0868 0.1927 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 0.3637 327.417 300.688 0.660 0.995 0.386 11.894-9.307 99.02 97 4 0.1751 524.546 512.336 0.942 0.999 0.342 9.237-7.194 100.00 213 7 0.1990 428.974 421.426 0.992 1.000 0.310 7.162-5.571 100.00 427 22 0.1893 321.893 314.426 0.974 1.001 0.310 5.546-4.326 100.00 867 58 0.0962 441.913 436.465 0.989 1.001 0.260 4.315-3.360 100.00 1859 96 0.0574 420.264 419.790 1.049 1.002 0.220 3.356-3.002 100.00 1373 60 0.0479 323.705 323.248 1.032 1.002 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.1634 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0868 r_free=0.1927 After: r_work=0.0871 r_free=0.1926 ================================== NQH flips ================================== r_work=0.0871 r_free=0.1926 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0871 r_free=0.1926 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0871 r_free=0.1926 | n_water=220 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0891 r_free=0.1916 | n_water=214 | time (s): 17.740 (total time: 18.400) Filter (q & B) r_work=0.0998 r_free=0.1902 | n_water=211 | time (s): 1.350 (total time: 19.750) Compute maps r_work=0.0998 r_free=0.1902 | n_water=211 | time (s): 0.510 (total time: 20.260) Filter (map) r_work=0.1235 r_free=0.1994 | n_water=150 | time (s): 1.440 (total time: 21.700) Find peaks r_work=0.1235 r_free=0.1994 | n_water=150 | time (s): 0.510 (total time: 22.210) Add new water r_work=0.1528 r_free=0.2235 | n_water=217 | time (s): 1.560 (total time: 23.770) Refine new water occ: r_work=0.0989 r_free=0.1880 adp: r_work=0.0980 r_free=0.1904 occ: r_work=0.0973 r_free=0.1884 adp: r_work=0.0973 r_free=0.1895 occ: r_work=0.0966 r_free=0.1875 adp: r_work=0.0966 r_free=0.1885 ADP+occupancy (water only), MIN, final r_work=0.0966 r_free=0.1885 r_work=0.0966 r_free=0.1885 | n_water=217 | time (s): 10.360 (total time: 34.130) Filter (q & B) r_work=0.0967 r_free=0.1884 | n_water=214 | time (s): 1.700 (total time: 35.830) Filter (dist only) r_work=0.0972 r_free=0.1891 | n_water=212 | time (s): 18.350 (total time: 54.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.951181 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.209638 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 0.0912 0.1872 0.0961 0.010 1.1 8.0 0.5 0.6 0 0.476 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.12 18.72 9.61 8.071 18.127 0.210 5.043 8.95 18.64 9.69 8.720 18.195 0.210 4.998 Individual atomic B min max mean iso aniso Overall: 0.00 108.27 16.60 11.45 1739 0 Protein: 0.00 108.27 15.72 11.43 1519 0 Water: 0.00 60.18 22.48 N/A 212 0 Other: 14.60 46.06 27.74 N/A 8 0 Chain A: 0.00 108.27 16.14 N/A 1633 0 Chain S: 0.00 60.18 23.76 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.83 656 10.83 - 21.65 647 21.65 - 32.48 255 32.48 - 43.31 110 43.31 - 54.14 34 54.14 - 64.96 16 64.96 - 75.79 11 75.79 - 86.62 6 86.62 - 97.44 2 97.44 - 108.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.0895 r_free=0.1864 r_work=0.0898 r_free=0.1864 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1864 target_work(ml) = 5.001 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0891 r_free = 0.1849 target_work(ml) = 4.997 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0891 r_free= 0.1849 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.996598 | | target function (ml) not normalized (work): 24598.253723 | | target function (ml) not normalized (free): 2101.657461 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1237 0.1801 5.5265 6.1907| | 2: 3.78 - 3.00 1.00 2430 110 0.0469 0.1932 4.453 11.114| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.92 11.77 1.00 1.00 12556.07| | 2: 3.78 - 3.00 2430 110 0.99 2.16 1.00 1.02 1065.21| |alpha: min = 0.99 max = 1.02 mean = 1.01| |beta: min = 701.53 max = 20703.28 mean = 6884.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.70 mean = 7.03| |phase err.(test): min = 0.00 max = 88.71 mean = 7.66| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0939 0.0891 0.1849 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2251 0.2262 0.2198 n_refl.: 5175 remove outliers: r(all,work,free)=0.2251 0.2262 0.2198 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2251 0.2262 0.2198 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0939 0.0892 0.1849 n_refl.: 5175 remove outliers: r(all,work,free)=0.0939 0.0892 0.1849 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 0.3760 327.417 294.990 0.620 0.989 0.360 11.894-9.307 99.02 97 4 0.1794 524.546 513.839 0.962 0.995 0.335 9.237-7.194 100.00 213 7 0.2085 428.974 420.988 1.003 0.998 0.310 7.162-5.571 100.00 427 22 0.1977 321.893 315.168 0.987 0.999 0.310 5.546-4.326 100.00 867 58 0.1013 441.913 435.463 1.004 1.001 0.280 4.315-3.360 100.00 1859 96 0.0587 420.264 420.602 1.073 1.003 0.230 3.356-3.002 100.00 1373 60 0.0454 323.705 323.011 1.056 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.2751 ================= 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 : 0.3620 0.1996 0.082 5.380 8.8 119.3 19.9 258 0.000 1_bss: 0.1552 0.1547 0.082 5.380 6.0 116.5 17.0 258 0.000 1_settarget: 0.1552 0.1547 0.082 5.380 6.0 116.5 17.0 258 0.000 1_nqh: 0.1552 0.1547 0.082 5.380 6.0 116.5 17.0 258 0.000 1_weight: 0.1552 0.1547 0.082 5.380 6.0 116.5 17.0 258 0.000 1_xyzrec: 0.1171 0.1787 0.010 0.982 6.0 116.5 17.0 258 0.199 1_adp: 0.1029 0.1791 0.010 0.982 2.2 111.7 17.4 258 0.199 1_regHadp: 0.1023 0.1799 0.010 0.982 2.2 111.7 17.4 258 0.199 1_occ: 0.1019 0.1788 0.010 0.982 2.2 111.7 17.4 258 0.199 2_bss: 0.1019 0.1774 0.010 0.982 1.3 110.8 16.4 258 0.199 2_settarget: 0.1019 0.1774 0.010 0.982 1.3 110.8 16.4 258 0.199 2_updatecdl: 0.1019 0.1774 0.010 1.008 1.3 110.8 16.4 258 0.199 2_nqh: 0.1019 0.1773 0.010 1.008 1.3 110.8 16.4 258 0.202 2_sol: 0.1135 0.1639 0.010 1.008 1.0 110.8 15.8 224 n/a 2_weight: 0.1135 0.1639 0.010 1.008 1.0 110.8 15.8 224 n/a 2_xyzrec: 0.1012 0.1808 0.009 0.978 1.0 110.8 15.8 224 n/a 2_adp: 0.0945 0.1829 0.009 0.978 0.0 106.8 16.5 224 n/a 2_regHadp: 0.0943 0.1828 0.009 0.978 0.0 106.8 16.5 224 n/a 2_occ: 0.0940 0.1820 0.009 0.978 0.0 106.8 16.5 224 n/a 3_bss: 0.0942 0.1837 0.009 0.978 0.0 106.8 16.5 224 n/a 3_settarget: 0.0942 0.1837 0.009 0.978 0.0 106.8 16.5 224 n/a 3_updatecdl: 0.0942 0.1837 0.009 0.984 0.0 106.8 16.5 224 n/a 3_nqh: 0.0943 0.1840 0.009 0.984 0.0 106.8 16.5 224 n/a 3_sol: 0.1042 0.1823 0.009 0.984 0.0 106.8 16.4 227 n/a 3_weight: 0.1042 0.1823 0.009 0.984 0.0 106.8 16.4 227 n/a 3_xyzrec: 0.0937 0.1838 0.011 1.084 0.0 106.8 16.4 227 n/a 3_adp: 0.0896 0.1853 0.011 1.084 0.0 107.0 16.4 227 n/a 3_regHadp: 0.0902 0.1861 0.011 1.084 0.0 107.0 16.4 227 n/a 3_occ: 0.0889 0.1841 0.011 1.084 0.0 107.0 16.4 227 n/a 4_bss: 0.0883 0.1847 0.011 1.084 0.0 107.0 16.4 227 n/a 4_settarget: 0.0883 0.1847 0.011 1.084 0.0 107.0 16.4 227 n/a 4_updatecdl: 0.0883 0.1847 0.011 1.087 0.0 107.0 16.4 227 n/a 4_nqh: 0.0883 0.1847 0.011 1.087 0.0 107.0 16.4 227 n/a 4_sol: 0.0982 0.1844 0.011 1.087 0.0 107.0 16.3 220 n/a 4_weight: 0.0982 0.1844 0.011 1.087 0.0 107.0 16.3 220 n/a 4_xyzrec: 0.0902 0.1883 0.010 1.039 0.0 107.0 16.3 220 n/a 4_adp: 0.0880 0.1929 0.010 1.039 0.0 106.7 16.5 220 n/a 4_regHadp: 0.0884 0.1932 0.010 1.039 0.0 106.7 16.5 220 n/a 4_occ: 0.0869 0.1919 0.010 1.039 0.0 106.7 16.5 220 n/a 5_bss: 0.0868 0.1927 0.010 1.039 0.0 106.7 16.5 220 n/a 5_settarget: 0.0868 0.1927 0.010 1.039 0.0 106.7 16.5 220 n/a 5_updatecdl: 0.0868 0.1927 0.010 1.047 0.0 106.7 16.5 220 n/a 5_setrh: 0.0871 0.1926 0.010 1.047 0.0 106.7 16.5 220 n/a 5_nqh: 0.0871 0.1926 0.010 1.047 0.0 106.7 16.5 220 n/a 5_sol: 0.0972 0.1891 0.010 1.047 0.0 106.7 16.5 212 n/a 5_weight: 0.0972 0.1891 0.010 1.047 0.0 106.7 16.5 212 n/a 5_xyzrec: 0.0912 0.1872 0.010 1.095 0.0 106.7 16.5 212 n/a 5_adp: 0.0895 0.1864 0.010 1.095 0.0 108.3 16.6 212 n/a 5_regHadp: 0.0898 0.1864 0.010 1.095 0.0 108.3 16.6 212 n/a 5_occ: 0.0891 0.1849 0.010 1.095 0.0 108.3 16.6 212 n/a end: 0.0892 0.1849 0.010 1.095 0.0 108.3 16.6 212 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8315495_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8315495_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9100 Refinement macro-cycles (run) : 477.1200 Write final files (write_after_run_outputs) : 11.5700 Total : 491.6000 Total CPU time: 8.55 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:53 PST -0800 (1735492733.87 s) Start R-work = 0.1552, R-free = 0.1547 Final R-work = 0.0892, R-free = 0.1849 =============================================================================== Job complete usr+sys time: 521.30 seconds wall clock time: 9 minutes 3.16 seconds (543.16 seconds total)