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_8736282.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_8736282.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8736282.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" } 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 1 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: 2.15, per 1000 atoms: 0.64 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: 0.33 Conformation dependent library (CDL) restraints added in 159.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.61 - 0.87: 288 0.87 - 1.13: 1291 1.13 - 1.39: 588 1.39 - 1.65: 919 1.65 - 1.91: 67 Bond restraints: 3153 Sorted by residual: bond pdb=" CA PRO A 73 " pdb=" C PRO A 73 " ideal model delta sigma weight residual 1.521 1.318 0.203 1.20e-02 6.94e+03 2.87e+02 bond pdb=" C LEU A 185 " pdb=" O LEU A 185 " ideal model delta sigma weight residual 1.236 1.013 0.223 1.32e-02 5.74e+03 2.85e+02 bond pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " ideal model delta sigma weight residual 1.522 1.322 0.200 1.19e-02 7.06e+03 2.83e+02 bond pdb=" C VAL A 51 " pdb=" O VAL A 51 " ideal model delta sigma weight residual 1.237 1.417 -0.180 1.08e-02 8.57e+03 2.77e+02 bond pdb=" CA ILE A 31 " pdb=" C ILE A 31 " ideal model delta sigma weight residual 1.523 1.333 0.190 1.14e-02 7.69e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 3452 5.28 - 10.55: 1819 10.55 - 15.82: 448 15.82 - 21.09: 54 21.09 - 26.37: 4 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.35 108.99 14.36 9.50e-01 1.11e+00 2.28e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.57 135.23 -12.66 9.20e-01 1.18e+00 1.89e+02 angle pdb=" O GLY A 136 " pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 122.42 105.72 16.70 1.31e+00 5.83e-01 1.62e+02 angle pdb=" OE1 GLN A 95 " pdb=" CD GLN A 95 " pdb=" NE2 GLN A 95 " ideal model delta sigma weight residual 122.60 109.95 12.65 1.00e+00 1.00e+00 1.60e+02 angle pdb=" O VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " ideal model delta sigma weight residual 122.62 108.76 13.86 1.17e+00 7.31e-01 1.40e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.87: 1327 17.87 - 35.74: 100 35.74 - 53.61: 38 53.61 - 71.48: 15 71.48 - 89.35: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N VAL A 23 " pdb=" C VAL A 23 " pdb=" CA VAL A 23 " pdb=" CB VAL A 23 " ideal model delta harmonic sigma weight residual 123.40 104.71 18.69 0 2.50e+00 1.60e-01 5.59e+01 dihedral pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CA PHE A 119 " pdb=" CB PHE A 119 " ideal model delta harmonic sigma weight residual 122.80 140.50 -17.70 0 2.50e+00 1.60e-01 5.01e+01 dihedral pdb=" C BASN A 97 " pdb=" N BASN A 97 " pdb=" CA BASN A 97 " pdb=" CB BASN A 97 " ideal model delta harmonic sigma weight residual -122.60 -139.37 16.77 0 2.50e+00 1.60e-01 4.50e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.200: 92 0.200 - 0.397: 73 0.397 - 0.593: 41 0.593 - 0.789: 29 0.789 - 0.986: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PHE A 119 " pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CB PHE A 119 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CA VAL A 23 " pdb=" N VAL A 23 " pdb=" C VAL A 23 " pdb=" CB VAL A 23 " both_signs ideal model delta sigma weight residual False 2.44 3.36 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 3.39 -0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.077 2.00e-02 2.50e+03 5.81e-02 1.01e+02 pdb=" CG ATYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.101 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.008 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.061 9.50e-02 1.11e+02 6.84e-02 9.63e+01 pdb=" NE ARG A 145 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.077 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " -0.067 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.099 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.023 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.086 2.00e-02 2.50e+03 5.52e-02 9.13e+01 pdb=" CG PHE A 164 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.077 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1060 2.32 - 2.89: 8105 2.89 - 3.46: 10509 3.46 - 4.03: 15335 4.03 - 4.60: 21607 Nonbonded interactions: 56616 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.754 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.778 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.813 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.834 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.834 2.450 ... (remaining 56611 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_8736282_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= 0.3613 r_free= 0.2063 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468418 | | target function (ml) not normalized (work): 22029.301109 | | target function (ml) not normalized (free): 1157.482348 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3793 0.2237 4.8583 4.9179| | 2: 3.78 - 3.00 1.00 2430 110 0.3394 0.1768 4.0673 4.174| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.79 2500 142 0.50 48.76 0.83 0.13 6601.93| | 2: 3.78 - 3.00 2430 110 0.94 11.19 1.48 0.26 446.65| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 377.40 max = 12057.04 mean = 3567.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.97 mean = 30.25| |phase err.(test): min = 0.00 max = 89.97 mean = 32.88| |-----------------------------------------------------------------------------| ----------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 0.238 1557 Z= 5.499 Angle : 5.270 16.705 2118 Z= 3.642 Chirality : 0.390 0.986 243 Planarity : 0.033 0.085 284 Dihedral : 13.762 89.347 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 35.68 % 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: -3.01 (0.46), residues: 224 helix: -3.33 (0.31), residues: 103 sheet: -0.11 (0.89), residues: 28 loop : -0.66 (0.57), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.023 ARG A 145 TYR 0.087 0.040 TYR A 141 PHE 0.109 0.040 PHE A 164 HIS 0.107 0.036 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= 0.3613 r_free= 0.2063 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468418 | | target function (ml) not normalized (work): 22029.301109 | | target function (ml) not normalized (free): 1157.482348 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3571 0.3647 0.2129 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3571 0.3647 0.2129 n_refl.: 5182 remove outliers: r(all,work,free)=0.2520 0.2542 0.2129 n_refl.: 5178 overall B=-2.60 to atoms: r(all,work,free)=0.2420 0.2439 0.2081 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1561 0.1560 0.1594 n_refl.: 5178 remove outliers: r(all,work,free)=0.1557 0.1555 0.1594 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 0.3903 449.996 404.319 0.648 1.060 0.408 11.894-9.307 99.02 97 4 0.1857 714.855 687.783 0.911 1.057 0.382 9.237-7.194 100.00 213 7 0.2173 584.609 572.033 0.944 1.051 0.367 7.162-5.571 100.00 427 22 0.2333 438.678 420.286 0.905 1.040 0.283 5.546-4.326 100.00 867 58 0.1394 602.243 592.904 0.951 1.022 0.220 4.315-3.360 100.00 1859 96 0.1314 572.739 567.255 1.028 0.991 0.199 3.356-3.002 100.00 1373 60 0.1563 441.148 436.736 1.040 0.961 0.096 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.5145 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1594 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1557 r_free=0.1589 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.644861 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.802004 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 0.1153 0.1804 0.0651 0.010 1.0 3.2 0.5 0.0 0 9.322 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 18.04 6.51 3.013 16.259 1.802 0.018 10.11 17.94 7.82 4.977 16.551 1.802 0.014 Individual atomic B min max mean iso aniso Overall: 2.58 111.70 17.84 5.30 1785 0 Protein: 2.58 111.29 15.15 5.29 1519 0 Water: 4.61 111.70 33.50 N/A 258 0 Other: 16.61 38.13 24.26 N/A 8 0 Chain A: 2.58 111.70 17.84 N/A 1785 0 Histogram: Values Number of atoms 2.58 - 13.49 918 13.49 - 24.40 479 24.40 - 35.31 191 35.31 - 46.22 111 46.22 - 57.14 52 57.14 - 68.05 17 68.05 - 78.96 8 78.96 - 89.87 5 89.87 - 100.79 1 100.79 - 111.70 3 =========================== Idealize ADP of riding H ========================== r_work=0.1011 r_free=0.1794 r_work=0.1005 r_free=0.1798 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1005 r_free = 0.1798 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 = 0.1005 r_free = 0.1796 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= 0.1005 r_free= 0.1796 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013792 | | target function (ls_wunit_k1) not normalized (work): 67.913258 | | target function (ls_wunit_k1) not normalized (free): 10.521077 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1045 0.1005 0.1796 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2113 0.2110 0.2260 n_refl.: 5176 remove outliers: r(all,work,free)=0.2113 0.2110 0.2260 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2071 0.2067 0.2247 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1009 0.1801 n_refl.: 5176 remove outliers: r(all,work,free)=0.1048 0.1007 0.1801 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 0.3319 316.120 299.181 0.641 1.011 0.369 11.894-9.307 99.02 97 4 0.1557 506.448 497.970 0.943 1.012 0.361 9.237-7.194 100.00 213 7 0.1685 414.174 412.947 0.988 1.011 0.341 7.162-5.571 100.00 427 22 0.1608 310.787 308.270 0.948 1.009 0.282 5.546-4.326 100.00 867 58 0.0904 426.666 423.986 0.963 1.005 0.202 4.315-3.360 100.00 1859 96 0.0762 405.764 405.558 1.017 0.998 0.193 3.356-3.002 100.00 1373 60 0.0992 312.537 310.898 0.997 0.992 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.2709 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1007 r_free=0.1801 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1010 r_free=0.1806 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1806 | n_water=258 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.1042 r_free=0.1802 | n_water=247 | time (s): 19.480 (total time: 20.010) Filter (q & B) r_work=0.1041 r_free=0.1802 | n_water=244 | time (s): 1.880 (total time: 21.890) Compute maps r_work=0.1041 r_free=0.1802 | n_water=244 | time (s): 0.530 (total time: 22.420) Filter (map) r_work=0.1349 r_free=0.1895 | n_water=143 | time (s): 1.560 (total time: 23.980) Find peaks r_work=0.1349 r_free=0.1895 | n_water=143 | time (s): 0.620 (total time: 24.600) Add new water r_work=0.1696 r_free=0.2189 | n_water=230 | time (s): 1.520 (total time: 26.120) Refine new water occ: r_work=0.1165 r_free=0.1685 adp: r_work=0.1137 r_free=0.1698 occ: r_work=0.1134 r_free=0.1680 adp: r_work=0.1121 r_free=0.1685 occ: r_work=0.1120 r_free=0.1665 adp: r_work=0.1117 r_free=0.1672 ADP+occupancy (water only), MIN, final r_work=0.1117 r_free=0.1672 r_work=0.1117 r_free=0.1672 | n_water=230 | time (s): 6.960 (total time: 33.080) Filter (q & B) r_work=0.1117 r_free=0.1672 | n_water=230 | time (s): 0.930 (total time: 34.010) Filter (dist only) r_work=0.1120 r_free=0.1677 | n_water=227 | time (s): 17.830 (total time: 51.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.556840 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.481740 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 0.1009 0.1759 0.0750 0.009 1.0 5.4 0.5 0.6 0 11.278 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.09 17.59 7.50 4.692 17.248 2.482 0.014 9.42 18.01 8.58 5.542 17.735 2.482 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 105.98 17.22 6.51 1754 0 Protein: 0.00 105.98 15.66 6.48 1519 0 Water: 0.00 63.03 27.34 N/A 227 0 Other: 14.01 39.95 26.45 N/A 8 0 Chain A: 0.00 105.98 16.33 N/A 1669 0 Chain S: 2.29 59.60 34.62 N/A 85 0 Histogram: Values Number of atoms 0.00 - 10.60 599 10.60 - 21.20 713 21.20 - 31.79 223 31.79 - 42.39 134 42.39 - 52.99 38 52.99 - 63.59 31 63.59 - 74.19 8 74.19 - 84.79 3 84.79 - 95.38 3 95.38 - 105.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.0942 r_free=0.1801 r_work=0.0940 r_free=0.1805 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0940 r_free = 0.1805 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0935 r_free = 0.1793 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0935 r_free= 0.1793 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011978 | | target function (ls_wunit_k1) not normalized (work): 58.969964 | | target function (ls_wunit_k1) not normalized (free): 9.704467 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0979 0.0935 0.1793 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2148 0.2151 0.2226 n_refl.: 5175 remove outliers: r(all,work,free)=0.2148 0.2151 0.2226 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2148 0.2151 0.2226 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0977 0.0934 0.1799 n_refl.: 5175 remove outliers: r(all,work,free)=0.0977 0.0934 0.1799 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 0.3336 316.120 297.502 0.643 1.000 0.364 11.894-9.307 99.02 97 4 0.1387 506.448 500.292 0.951 1.003 0.350 9.237-7.194 100.00 213 7 0.1455 414.174 412.304 0.991 1.003 0.340 7.162-5.571 100.00 427 22 0.1391 310.787 307.849 0.967 1.003 0.290 5.546-4.326 100.00 867 58 0.0782 426.666 423.724 0.979 1.002 0.230 4.315-3.360 100.00 1859 96 0.0718 405.764 405.779 1.031 1.001 0.190 3.356-3.002 100.00 1373 60 0.0989 312.537 312.670 1.011 0.999 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-5.2052 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0934 r_free=0.1799 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0937 r_free=0.1806 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0937 r_free=0.1806 | n_water=227 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0957 r_free=0.1785 | n_water=222 | time (s): 18.160 (total time: 18.630) Filter (q & B) r_work=0.1014 r_free=0.1804 | n_water=220 | time (s): 1.270 (total time: 19.900) Compute maps r_work=0.1014 r_free=0.1804 | n_water=220 | time (s): 0.430 (total time: 20.330) Filter (map) r_work=0.1292 r_free=0.1881 | n_water=147 | time (s): 1.780 (total time: 22.110) Find peaks r_work=0.1292 r_free=0.1881 | n_water=147 | time (s): 0.630 (total time: 22.740) Add new water r_work=0.1679 r_free=0.2233 | n_water=234 | time (s): 1.760 (total time: 24.500) Refine new water occ: r_work=0.1083 r_free=0.1727 adp: r_work=0.1080 r_free=0.1745 occ: r_work=0.1066 r_free=0.1720 adp: r_work=0.1068 r_free=0.1733 occ: r_work=0.1056 r_free=0.1712 adp: r_work=0.1057 r_free=0.1726 ADP+occupancy (water only), MIN, final r_work=0.1057 r_free=0.1726 r_work=0.1057 r_free=0.1726 | n_water=234 | time (s): 8.650 (total time: 33.150) Filter (q & B) r_work=0.1057 r_free=0.1726 | n_water=234 | time (s): 0.880 (total time: 34.030) Filter (dist only) r_work=0.1057 r_free=0.1729 | n_water=233 | time (s): 18.960 (total time: 52.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.119330 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.176505 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 0.0951 0.1818 0.0867 0.011 1.1 4.8 0.5 0.6 0 0.560 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.51 18.18 8.67 5.465 18.447 0.177 5.134 9.08 17.97 8.88 7.209 18.441 0.177 5.039 Individual atomic B min max mean iso aniso Overall: 0.00 103.52 16.95 8.79 1760 0 Protein: 0.00 103.52 15.70 8.78 1519 0 Water: 0.00 58.03 24.70 N/A 233 0 Other: 19.21 43.65 28.69 N/A 8 0 Chain A: 0.00 103.52 16.35 N/A 1653 0 Chain S: 0.00 50.07 26.29 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.35 598 10.35 - 20.70 688 20.70 - 31.06 258 31.06 - 41.41 122 41.41 - 51.76 56 51.76 - 62.11 17 62.11 - 72.46 10 72.46 - 82.82 5 82.82 - 93.17 3 93.17 - 103.52 3 =========================== Idealize ADP of riding H ========================== r_work=0.0908 r_free=0.1797 r_work=0.0912 r_free=0.1805 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1805 target_work(ml) = 5.041 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0900 r_free = 0.1789 target_work(ml) = 5.033 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0900 r_free= 0.1789 coordinate error (max.-lik. estimate): 0.23 A | | | | normalized target function (ml) (work): 5.033498 | | target function (ml) not normalized (work): 24779.911853 | | target function (ml) not normalized (free): 1784.075291 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0944 0.0900 0.1789 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2176 0.2185 0.2197 n_refl.: 5175 remove outliers: r(all,work,free)=0.2176 0.2185 0.2197 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2176 0.2185 0.2197 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0935 0.0890 0.1787 n_refl.: 5175 remove outliers: r(all,work,free)=0.0932 0.0887 0.1787 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3631 318.223 282.347 0.580 0.996 0.330 11.894-9.307 99.02 97 4 0.1820 506.448 493.483 0.948 0.999 0.330 9.237-7.194 100.00 213 7 0.1894 414.174 407.090 1.005 1.000 0.299 7.162-5.571 100.00 427 22 0.1836 310.787 302.029 0.993 1.001 0.280 5.546-4.326 100.00 867 58 0.0913 426.666 421.986 1.010 1.002 0.230 4.315-3.360 100.00 1859 96 0.0577 405.764 405.275 1.076 1.003 0.200 3.356-3.002 100.00 1373 60 0.0629 312.537 312.432 1.055 1.004 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9172 b_overall=-7.3670 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0887 r_free=0.1787 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0887 r_free=0.1787 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0887 r_free=0.1787 | n_water=233 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0894 r_free=0.1775 | n_water=232 | time (s): 18.760 (total time: 19.310) Filter (q & B) r_work=0.0957 r_free=0.1793 | n_water=228 | time (s): 1.370 (total time: 20.680) Compute maps r_work=0.0957 r_free=0.1793 | n_water=228 | time (s): 0.440 (total time: 21.120) Filter (map) r_work=0.1240 r_free=0.1916 | n_water=151 | time (s): 1.240 (total time: 22.360) Find peaks r_work=0.1240 r_free=0.1916 | n_water=151 | time (s): 0.470 (total time: 22.830) Add new water r_work=0.1555 r_free=0.2185 | n_water=228 | time (s): 1.460 (total time: 24.290) Refine new water occ: r_work=0.1000 r_free=0.1792 adp: r_work=0.0995 r_free=0.1805 occ: r_work=0.0986 r_free=0.1788 adp: r_work=0.0987 r_free=0.1796 occ: r_work=0.0979 r_free=0.1780 adp: r_work=0.0979 r_free=0.1788 ADP+occupancy (water only), MIN, final r_work=0.0979 r_free=0.1788 r_work=0.0979 r_free=0.1788 | n_water=228 | time (s): 13.920 (total time: 38.210) Filter (q & B) r_work=0.0980 r_free=0.1794 | n_water=227 | time (s): 1.650 (total time: 39.860) Filter (dist only) r_work=0.1001 r_free=0.1797 | n_water=224 | time (s): 17.300 (total time: 57.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.032201 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.226976 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 0.0910 0.1844 0.0934 0.011 1.1 5.4 0.5 0.0 0 0.516 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.10 18.44 9.34 6.889 18.456 0.227 5.022 8.87 18.86 9.99 8.397 18.602 0.227 4.955 Individual atomic B min max mean iso aniso Overall: 0.00 101.26 17.22 10.93 1751 0 Protein: 0.00 101.26 16.19 10.93 1519 0 Water: 0.00 58.62 23.82 N/A 224 0 Other: 19.54 46.50 28.24 N/A 8 0 Chain A: 0.00 101.26 16.73 N/A 1643 0 Chain S: 0.00 46.86 24.70 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.13 560 10.13 - 20.25 670 20.25 - 30.38 292 30.38 - 40.51 136 40.51 - 50.63 50 50.63 - 60.76 18 60.76 - 70.88 8 70.88 - 81.01 8 81.01 - 91.14 7 91.14 - 101.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.0887 r_free=0.1886 r_work=0.0891 r_free=0.1899 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0891 r_free = 0.1899 target_work(ml) = 4.960 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0882 r_free = 0.1887 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0882 r_free= 0.1887 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 4.954156 | | target function (ml) not normalized (work): 24384.354113 | | target function (ml) not normalized (free): 2110.583000 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0932 0.0882 0.1887 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2152 0.2150 0.2329 n_refl.: 5174 remove outliers: r(all,work,free)=0.2152 0.2150 0.2329 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2152 0.2150 0.2329 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0931 0.0881 0.1888 n_refl.: 5174 remove outliers: r(all,work,free)=0.0931 0.0881 0.1888 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3862 318.223 286.696 0.586 0.988 0.320 11.894-9.307 99.02 97 4 0.1945 506.448 489.110 0.944 0.993 0.320 9.237-7.194 100.00 213 7 0.2068 414.174 402.690 1.005 0.996 0.310 7.162-5.571 100.00 427 22 0.1964 310.787 301.099 1.001 0.997 0.290 5.546-4.326 100.00 867 58 0.0972 426.666 421.412 1.017 0.999 0.250 4.315-3.360 100.00 1859 96 0.0559 405.764 405.110 1.084 1.003 0.201 3.356-3.002 100.00 1373 60 0.0478 312.537 312.420 1.066 1.006 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8266 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0881 r_free=0.1888 After: r_work=0.0884 r_free=0.1888 ================================== NQH flips ================================== r_work=0.0884 r_free=0.1888 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=0.0885 r_free=0.1892 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0885 r_free=0.1892 | n_water=224 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0890 r_free=0.1895 | n_water=222 | time (s): 19.900 (total time: 20.470) Filter (q & B) r_work=0.0980 r_free=0.1891 | n_water=220 | time (s): 1.440 (total time: 21.910) Compute maps r_work=0.0980 r_free=0.1891 | n_water=220 | time (s): 0.650 (total time: 22.560) Filter (map) r_work=0.1265 r_free=0.1936 | n_water=153 | time (s): 1.510 (total time: 24.070) Find peaks r_work=0.1265 r_free=0.1936 | n_water=153 | time (s): 0.590 (total time: 24.660) Add new water r_work=0.1564 r_free=0.2242 | n_water=223 | time (s): 1.780 (total time: 26.440) Refine new water occ: r_work=0.1005 r_free=0.1906 adp: r_work=0.0996 r_free=0.1920 occ: r_work=0.0989 r_free=0.1908 adp: r_work=0.0988 r_free=0.1910 occ: r_work=0.0982 r_free=0.1897 adp: r_work=0.0981 r_free=0.1899 ADP+occupancy (water only), MIN, final r_work=0.0981 r_free=0.1899 r_work=0.0981 r_free=0.1899 | n_water=223 | time (s): 8.340 (total time: 34.780) Filter (q & B) r_work=0.0981 r_free=0.1903 | n_water=222 | time (s): 1.370 (total time: 36.150) Filter (dist only) r_work=0.0981 r_free=0.1903 | n_water=222 | time (s): 15.520 (total time: 51.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.969787 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.194496 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 0.0928 0.1904 0.0976 0.011 1.1 9.3 0.5 0.0 0 0.485 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.28 19.04 9.76 8.305 18.869 0.194 4.988 9.09 19.30 10.22 9.083 18.961 0.194 4.939 Individual atomic B min max mean iso aniso Overall: 0.00 106.87 17.46 12.03 1749 0 Protein: 0.00 106.87 16.53 12.02 1519 0 Water: 0.00 56.71 23.48 N/A 222 0 Other: 16.28 46.54 27.24 N/A 8 0 Chain A: 0.00 106.87 16.97 N/A 1633 0 Chain S: 0.00 51.24 24.42 N/A 116 0 Histogram: Values Number of atoms 0.00 - 10.69 589 10.69 - 21.37 666 21.37 - 32.06 290 32.06 - 42.75 122 42.75 - 53.43 45 53.43 - 64.12 13 64.12 - 74.81 8 74.81 - 85.49 8 85.49 - 96.18 6 96.18 - 106.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.0909 r_free=0.1930 r_work=0.0910 r_free=0.1931 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0910 r_free = 0.1931 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0904 r_free = 0.1921 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0904 r_free= 0.1921 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 4.938452 | | target function (ml) not normalized (work): 24307.058843 | | target function (ml) not normalized (free): 2216.624269 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1283 0.1917 5.51 6.1516| | 2: 3.78 - 3.00 1.00 2430 110 0.0442 0.1929 4.3524 12.21| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.91 12.42 1.00 0.95 12785.05| | 2: 3.78 - 3.00 2430 110 0.99 1.87 1.01 0.97 877.81| |alpha: min = 0.93 max = 0.97 mean = 0.96| |beta: min = 562.59 max = 21475.59 mean = 6906.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.84 mean = 7.21| |phase err.(test): min = 0.00 max = 89.71 mean = 7.71| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0954 0.0904 0.1921 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2193 0.2194 0.2317 n_refl.: 5174 remove outliers: r(all,work,free)=0.2193 0.2194 0.2317 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2193 0.2194 0.2317 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0954 0.0904 0.1913 n_refl.: 5174 remove outliers: r(all,work,free)=0.0954 0.0904 0.1913 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.4063 318.223 283.983 0.572 0.985 0.310 11.894-9.307 99.02 97 4 0.1996 506.448 489.457 0.954 0.992 0.317 9.237-7.194 100.00 213 7 0.2234 414.174 402.467 1.012 0.995 0.298 7.162-5.571 100.00 427 22 0.2039 310.787 300.897 1.006 0.997 0.280 5.546-4.326 100.00 867 58 0.1040 426.666 420.938 1.033 0.999 0.250 4.315-3.360 100.00 1859 96 0.0572 405.764 405.409 1.112 1.003 0.210 3.356-3.002 100.00 1373 60 0.0422 312.537 312.473 1.097 1.006 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-9.0838 ================= 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 : 0.3613 0.2063 0.082 5.270 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1594 0.082 5.270 6.2 116.7 17.3 258 0.000 1_settarget: 0.1555 0.1594 0.082 5.270 6.2 116.7 17.3 258 0.000 1_nqh: 0.1557 0.1589 0.082 5.270 6.2 116.7 17.3 258 0.009 1_weight: 0.1557 0.1589 0.082 5.270 6.2 116.7 17.3 258 0.009 1_xyzrec: 0.1153 0.1804 0.010 0.972 6.2 116.7 17.3 258 0.218 1_adp: 0.1011 0.1794 0.010 0.972 2.6 111.7 17.8 258 0.218 1_regHadp: 0.1005 0.1798 0.010 0.972 2.6 111.7 17.8 258 0.218 1_occ: 0.1005 0.1796 0.010 0.972 2.6 111.7 17.8 258 0.218 2_bss: 0.1007 0.1801 0.010 0.972 1.6 110.7 16.9 258 0.218 2_settarget: 0.1007 0.1801 0.010 0.972 1.6 110.7 16.9 258 0.218 2_updatecdl: 0.1007 0.1801 0.010 0.986 1.6 110.7 16.9 258 0.218 2_nqh: 0.1010 0.1806 0.010 0.986 1.6 110.7 16.9 258 0.213 2_sol: 0.1120 0.1677 0.010 0.986 1.0 110.3 16.3 227 n/a 2_weight: 0.1120 0.1677 0.010 0.986 1.0 110.3 16.3 227 n/a 2_xyzrec: 0.1009 0.1759 0.009 0.969 1.0 110.3 16.3 227 n/a 2_adp: 0.0942 0.1801 0.009 0.969 0.0 106.0 17.2 227 n/a 2_regHadp: 0.0940 0.1805 0.009 0.969 0.0 106.0 17.2 227 n/a 2_occ: 0.0935 0.1793 0.009 0.969 0.0 106.0 17.2 227 n/a 3_bss: 0.0934 0.1799 0.009 0.969 0.0 106.0 17.2 227 n/a 3_settarget: 0.0934 0.1799 0.009 0.969 0.0 106.0 17.2 227 n/a 3_updatecdl: 0.0934 0.1799 0.009 0.977 0.0 106.0 17.2 227 n/a 3_nqh: 0.0937 0.1806 0.009 0.977 0.0 106.0 17.2 227 n/a 3_sol: 0.1057 0.1729 0.009 0.977 0.0 106.0 17.0 233 n/a 3_weight: 0.1057 0.1729 0.009 0.977 0.0 106.0 17.0 233 n/a 3_xyzrec: 0.0951 0.1818 0.011 1.056 0.0 106.0 17.0 233 n/a 3_adp: 0.0908 0.1797 0.011 1.056 0.0 103.5 17.0 233 n/a 3_regHadp: 0.0912 0.1805 0.011 1.056 0.0 103.5 17.0 233 n/a 3_occ: 0.0900 0.1789 0.011 1.056 0.0 103.5 17.0 233 n/a 4_bss: 0.0887 0.1787 0.011 1.056 0.0 103.5 17.0 233 n/a 4_settarget: 0.0887 0.1787 0.011 1.056 0.0 103.5 17.0 233 n/a 4_updatecdl: 0.0887 0.1787 0.011 1.068 0.0 103.5 17.0 233 n/a 4_nqh: 0.0887 0.1787 0.011 1.068 0.0 103.5 17.0 233 n/a 4_sol: 0.1001 0.1797 0.011 1.068 0.0 103.5 16.9 224 n/a 4_weight: 0.1001 0.1797 0.011 1.068 0.0 103.5 16.9 224 n/a 4_xyzrec: 0.0910 0.1844 0.011 1.063 0.0 103.5 16.9 224 n/a 4_adp: 0.0887 0.1886 0.011 1.063 0.0 101.3 17.2 224 n/a 4_regHadp: 0.0891 0.1899 0.011 1.063 0.0 101.3 17.2 224 n/a 4_occ: 0.0882 0.1887 0.011 1.063 0.0 101.3 17.2 224 n/a 5_bss: 0.0881 0.1888 0.011 1.063 0.0 101.3 17.2 224 n/a 5_settarget: 0.0881 0.1888 0.011 1.063 0.0 101.3 17.2 224 n/a 5_updatecdl: 0.0881 0.1888 0.011 1.057 0.0 101.3 17.2 224 n/a 5_setrh: 0.0884 0.1888 0.011 1.057 0.0 101.3 17.2 224 n/a 5_nqh: 0.0885 0.1892 0.011 1.057 0.0 101.3 17.2 224 n/a 5_sol: 0.0981 0.1903 0.011 1.057 0.0 101.3 17.3 222 n/a 5_weight: 0.0981 0.1903 0.011 1.057 0.0 101.3 17.3 222 n/a 5_xyzrec: 0.0928 0.1904 0.011 1.103 0.0 101.3 17.3 222 n/a 5_adp: 0.0909 0.1930 0.011 1.103 0.0 106.9 17.5 222 n/a 5_regHadp: 0.0910 0.1931 0.011 1.103 0.0 106.9 17.5 222 n/a 5_occ: 0.0904 0.1921 0.011 1.103 0.0 106.9 17.5 222 n/a end: 0.0904 0.1913 0.011 1.103 0.0 106.9 17.5 222 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8736282_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8736282_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5900 Refinement macro-cycles (run) : 490.1200 Write final files (write_after_run_outputs) : 9.8100 Total : 503.5200 Total CPU time: 8.77 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:06 PST -0800 (1735492746.86 s) Start R-work = 0.1555, R-free = 0.1594 Final R-work = 0.0904, R-free = 0.1913 =============================================================================== Job complete usr+sys time: 533.63 seconds wall clock time: 9 minutes 15.44 seconds (555.44 seconds total)