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_8498250.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_8498250.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8498250.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 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: 1.54, per 1000 atoms: 0.46 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: 0.38 Conformation dependent library (CDL) restraints added in 189.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 524 0.91 - 1.17: 1127 1.17 - 1.42: 638 1.42 - 1.68: 824 1.68 - 1.93: 40 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 1.237 0.948 0.289 1.16e-02 7.43e+03 6.19e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.512 -0.191 1.00e-02 1.00e+04 3.65e+02 bond pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 1.331 1.522 -0.191 1.05e-02 9.07e+03 3.32e+02 bond pdb=" N SER A 142 " pdb=" CA SER A 142 " ideal model delta sigma weight residual 1.455 1.231 0.224 1.25e-02 6.40e+03 3.21e+02 bond pdb=" CA ALA A 165 " pdb=" C ALA A 165 " ideal model delta sigma weight residual 1.524 1.300 0.224 1.29e-02 6.01e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.97: 3296 4.97 - 9.94: 1848 9.94 - 14.91: 558 14.91 - 19.88: 72 19.88 - 24.85: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 95.86 13.14 1.00e+00 1.00e+00 1.73e+02 angle pdb=" O ALA A 171 " pdb=" C ALA A 171 " pdb=" N LEU A 172 " ideal model delta sigma weight residual 122.27 138.23 -15.96 1.23e+00 6.61e-01 1.68e+02 angle pdb=" OD1BASN A 76 " pdb=" CG BASN A 76 " pdb=" ND2BASN A 76 " ideal model delta sigma weight residual 122.60 135.57 -12.97 1.00e+00 1.00e+00 1.68e+02 angle pdb=" CA LEU A 92 " pdb=" C LEU A 92 " pdb=" N ALYS A 93 " ideal model delta sigma weight residual 117.39 101.55 15.84 1.24e+00 6.50e-01 1.63e+02 angle pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " ideal model delta sigma weight residual 115.61 102.52 13.09 1.03e+00 9.43e-01 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 15.72: 1270 15.72 - 31.43: 154 31.43 - 47.13: 31 47.13 - 62.84: 22 62.84 - 78.55: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual 122.80 144.78 -21.98 0 2.50e+00 1.60e-01 7.73e+01 dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -142.28 19.68 0 2.50e+00 1.60e-01 6.19e+01 dihedral pdb=" C HIS A 138 " pdb=" N HIS A 138 " pdb=" CA HIS A 138 " pdb=" CB HIS A 138 " ideal model delta harmonic sigma weight residual -122.60 -141.26 18.66 0 2.50e+00 1.60e-01 5.57e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 115 0.253 - 0.506: 72 0.506 - 0.759: 40 0.759 - 1.011: 12 1.011 - 1.264: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 72 " pdb=" CB LEU A 72 " pdb=" CD1 LEU A 72 " pdb=" CD2 LEU A 72 " both_signs ideal model delta sigma weight residual False -2.59 -3.85 1.26 2.00e-01 2.50e+01 4.00e+01 chirality pdb=" CA HIS A 138 " pdb=" N HIS A 138 " pdb=" C HIS A 138 " pdb=" CB HIS A 138 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.77e+01 chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.49 1.03 2.00e-01 2.50e+01 2.67e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.006 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG TYR A 141 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.138 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.137 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.094 2.00e-02 2.50e+03 7.07e-02 1.12e+02 pdb=" CG HIS A 126 " -0.124 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.043 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.018 2.00e-02 2.50e+03 5.86e-02 1.03e+02 pdb=" CG PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.114 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.113 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.064 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 620 2.25 - 2.84: 7617 2.84 - 3.42: 10668 3.42 - 4.01: 15427 4.01 - 4.60: 22287 Nonbonded interactions: 56619 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.662 2.100 nonbonded pdb=" O GLY A 37 " pdb=" H LEU A 58 " model vdw 1.810 2.450 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.853 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.865 2.450 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.875 2.270 ... (remaining 56614 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_8498250_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= 0.3622 r_free= 0.2042 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471243 | | target function (ml) not normalized (work): 22043.225815 | | target function (ml) not normalized (free): 1157.541210 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3807 0.2234 4.848 4.9076| | 2: 3.78 - 3.00 1.00 2430 110 0.3395 0.1716 4.0836 4.1879| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.82 0.83 0.13 6604.28| | 2: 3.78 - 3.00 2430 110 0.94 11.30 1.48 0.26 453.42| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 390.68 max = 12077.43 mean = 3572.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.32| |phase err.(test): min = 0.00 max = 89.96 mean = 33.33| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.289 1557 Z= 5.583 Angle : 5.285 17.694 2118 Z= 3.771 Chirality : 0.415 1.264 243 Planarity : 0.033 0.111 284 Dihedral : 13.679 78.546 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.81 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.44), residues: 224 helix: -2.54 (0.34), residues: 108 sheet: -0.48 (0.92), residues: 28 loop : -0.44 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.020 ARG A 5 TYR 0.091 0.043 TYR A 141 PHE 0.105 0.045 PHE A 162 HIS 0.081 0.050 HIS A 115 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= 0.3622 r_free= 0.2042 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471243 | | target function (ml) not normalized (work): 22043.225815 | | target function (ml) not normalized (free): 1157.541210 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3579 0.3656 0.2159 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3579 0.3656 0.2159 n_refl.: 5182 remove outliers: r(all,work,free)=0.2533 0.2555 0.2159 n_refl.: 5178 overall B=-2.91 to atoms: r(all,work,free)=0.2423 0.2442 0.2129 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1570 0.1565 0.1679 n_refl.: 5178 remove outliers: r(all,work,free)=0.1566 0.1561 0.1679 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 0.3838 449.889 411.114 0.657 1.076 0.404 11.894-9.307 99.02 97 4 0.1853 714.684 692.291 0.936 1.071 0.393 9.237-7.194 100.00 213 7 0.2218 584.470 573.771 0.965 1.063 0.354 7.162-5.571 100.00 427 22 0.2352 438.573 423.558 0.930 1.050 0.304 5.546-4.326 100.00 867 58 0.1403 602.099 594.388 0.981 1.027 0.268 4.315-3.360 100.00 1859 96 0.1279 572.603 566.293 1.057 0.989 0.200 3.356-3.002 100.00 1373 60 0.1629 441.043 434.706 1.074 0.951 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.7286 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1561 r_free=0.1679 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1561 r_free=0.1679 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.626537 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.983938 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1161 0.1784 0.0624 0.010 1.0 2.9 0.5 0.0 0 9.813 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 17.84 6.24 3.013 15.944 1.984 0.018 10.19 17.78 7.59 4.946 16.134 1.984 0.014 Individual atomic B min max mean iso aniso Overall: 2.17 111.38 17.33 5.32 1785 0 Protein: 2.17 110.66 14.64 5.31 1519 0 Water: 3.96 111.38 32.98 N/A 258 0 Other: 16.75 38.29 24.36 N/A 8 0 Chain A: 2.17 111.38 17.33 N/A 1785 0 Histogram: Values Number of atoms 2.17 - 13.09 916 13.09 - 24.01 482 24.01 - 34.93 189 34.93 - 45.85 111 45.85 - 56.77 56 56.77 - 67.70 14 67.70 - 78.62 8 78.62 - 89.54 5 89.54 - 100.46 1 100.46 - 111.38 3 =========================== Idealize ADP of riding H ========================== r_work=0.1019 r_free=0.1778 r_work=0.1014 r_free=0.1783 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1014 r_free = 0.1783 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 = 0.1010 r_free = 0.1782 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 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= 0.1010 r_free= 0.1782 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013822 | | target function (ls_wunit_k1) not normalized (work): 68.058803 | | target function (ls_wunit_k1) not normalized (free): 10.499302 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1049 0.1010 0.1782 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2094 0.2093 0.2214 n_refl.: 5176 remove outliers: r(all,work,free)=0.2094 0.2093 0.2214 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2054 0.2052 0.2203 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1010 0.1780 n_refl.: 5176 remove outliers: r(all,work,free)=0.1049 0.1010 0.1780 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 0.3336 330.889 313.338 0.672 1.024 0.386 11.894-9.307 99.02 97 4 0.1547 525.643 516.824 0.975 1.023 0.369 9.237-7.194 100.00 213 7 0.1656 429.872 430.008 1.009 1.021 0.310 7.162-5.571 100.00 427 22 0.1637 322.566 319.340 0.967 1.016 0.292 5.546-4.326 100.00 867 58 0.0918 442.838 439.589 0.994 1.009 0.242 4.315-3.360 100.00 1859 96 0.0758 421.144 421.041 1.043 0.996 0.193 3.356-3.002 100.00 1373 60 0.0994 324.382 322.866 1.027 0.983 0.084 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4104 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1010 r_free=0.1780 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1010 r_free=0.1780 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1780 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1038 r_free=0.1767 | n_water=247 | time (s): 19.110 (total time: 19.770) Filter (q & B) r_work=0.1038 r_free=0.1770 | n_water=244 | time (s): 1.390 (total time: 21.160) Compute maps r_work=0.1038 r_free=0.1770 | n_water=244 | time (s): 0.480 (total time: 21.640) Filter (map) r_work=0.1348 r_free=0.1816 | n_water=142 | time (s): 1.410 (total time: 23.050) Find peaks r_work=0.1348 r_free=0.1816 | n_water=142 | time (s): 0.440 (total time: 23.490) Add new water r_work=0.1683 r_free=0.2082 | n_water=221 | time (s): 1.470 (total time: 24.960) Refine new water occ: r_work=0.1158 r_free=0.1669 adp: r_work=0.1141 r_free=0.1686 occ: r_work=0.1136 r_free=0.1661 adp: r_work=0.1129 r_free=0.1671 occ: r_work=0.1128 r_free=0.1667 adp: r_work=0.1127 r_free=0.1668 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1668 r_work=0.1127 r_free=0.1668 | n_water=221 | time (s): 3.170 (total time: 28.130) Filter (q & B) r_work=0.1127 r_free=0.1668 | n_water=221 | time (s): 1.040 (total time: 29.170) Filter (dist only) r_work=0.1133 r_free=0.1671 | n_water=219 | time (s): 15.890 (total time: 45.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.229668 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.823072 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 0.1033 0.1740 0.0708 0.009 0.9 3.8 0.5 0.6 0 10.615 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.33 17.40 7.08 4.675 16.625 2.823 0.014 9.66 18.02 8.36 5.473 17.029 2.823 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.50 16.35 6.54 1746 0 Protein: 0.00 107.50 14.93 6.51 1519 0 Water: 0.00 64.01 25.83 N/A 219 0 Other: 10.80 45.17 28.06 N/A 8 0 Chain A: 0.00 107.50 15.66 N/A 1667 0 Chain S: 5.34 57.34 30.92 N/A 79 0 Histogram: Values Number of atoms 0.00 - 10.75 707 10.75 - 21.50 649 21.50 - 32.25 201 32.25 - 43.00 113 43.00 - 53.75 39 53.75 - 64.50 24 64.50 - 75.25 6 75.25 - 86.00 2 86.00 - 96.75 3 96.75 - 107.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.0966 r_free=0.1802 r_work=0.0963 r_free=0.1807 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0963 r_free = 0.1807 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0957 r_free = 0.1798 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.25 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= 0.0957 r_free= 0.1798 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.012557 | | target function (ls_wunit_k1) not normalized (work): 61.830524 | | target function (ls_wunit_k1) not normalized (free): 10.038433 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1000 0.0957 0.1798 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2142 0.2145 0.2207 n_refl.: 5176 remove outliers: r(all,work,free)=0.2142 0.2145 0.2207 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2142 0.2145 0.2207 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1001 0.0958 0.1807 n_refl.: 5176 remove outliers: r(all,work,free)=0.1001 0.0958 0.1807 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3337 330.889 312.518 0.679 1.028 0.381 11.894-9.307 99.02 97 4 0.1484 525.643 520.117 0.960 1.028 0.340 9.237-7.194 100.00 213 7 0.1513 429.872 430.319 1.000 1.025 0.320 7.162-5.571 100.00 427 22 0.1447 322.566 321.398 0.974 1.020 0.300 5.546-4.326 100.00 867 58 0.0809 442.838 439.929 1.000 1.010 0.260 4.315-3.360 100.00 1859 96 0.0743 421.144 420.925 1.054 0.995 0.200 3.356-3.002 100.00 1373 60 0.0978 324.382 323.404 1.045 0.979 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.9428 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0958 r_free=0.1807 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0957 r_free=0.1808 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0957 r_free=0.1808 | n_water=219 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0978 r_free=0.1817 | n_water=214 | time (s): 17.660 (total time: 18.220) Filter (q & B) r_work=0.1038 r_free=0.1821 | n_water=212 | time (s): 1.380 (total time: 19.600) Compute maps r_work=0.1038 r_free=0.1821 | n_water=212 | time (s): 0.480 (total time: 20.080) Filter (map) r_work=0.1291 r_free=0.1888 | n_water=144 | time (s): 1.460 (total time: 21.540) Find peaks r_work=0.1291 r_free=0.1888 | n_water=144 | time (s): 0.530 (total time: 22.070) Add new water r_work=0.1670 r_free=0.2287 | n_water=228 | time (s): 1.390 (total time: 23.460) Refine new water occ: r_work=0.1085 r_free=0.1831 adp: r_work=0.1080 r_free=0.1846 occ: r_work=0.1067 r_free=0.1817 adp: r_work=0.1066 r_free=0.1828 occ: r_work=0.1054 r_free=0.1800 adp: r_work=0.1054 r_free=0.1810 ADP+occupancy (water only), MIN, final r_work=0.1054 r_free=0.1810 r_work=0.1054 r_free=0.1810 | n_water=228 | time (s): 14.190 (total time: 37.650) Filter (q & B) r_work=0.1055 r_free=0.1809 | n_water=226 | time (s): 1.450 (total time: 39.100) Filter (dist only) r_work=0.1069 r_free=0.1809 | n_water=224 | time (s): 15.910 (total time: 55.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.117583 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.271317 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 0.0968 0.1815 0.0846 0.011 1.0 4.5 0.5 0.0 0 0.559 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.68 18.15 8.46 5.450 17.751 0.271 5.188 9.23 18.42 9.18 7.240 17.731 0.271 5.098 Individual atomic B min max mean iso aniso Overall: 0.00 107.65 16.26 8.91 1751 0 Protein: 0.00 107.65 15.04 8.88 1519 0 Water: 0.00 59.01 24.09 N/A 224 0 Other: 11.28 45.98 27.89 N/A 8 0 Chain A: 0.00 107.65 15.65 N/A 1651 0 Chain S: 0.00 56.28 26.37 N/A 100 0 Histogram: Values Number of atoms 0.00 - 10.77 682 10.77 - 21.53 668 21.53 - 32.30 217 32.30 - 43.06 114 43.06 - 53.83 33 53.83 - 64.59 21 64.59 - 75.36 9 75.36 - 86.12 2 86.12 - 96.89 4 96.89 - 107.65 1 =========================== Idealize ADP of riding H ========================== r_work=0.0923 r_free=0.1842 r_work=0.0929 r_free=0.1855 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0929 r_free = 0.1855 target_work(ml) = 5.102 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0916 r_free = 0.1837 target_work(ml) = 5.094 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0916 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.093742 | | target function (ml) not normalized (work): 25081.583347 | | target function (ml) not normalized (free): 1799.632329 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0963 0.0916 0.1837 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2156 0.2167 0.2119 n_refl.: 5176 remove outliers: r(all,work,free)=0.2156 0.2167 0.2119 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2156 0.2167 0.2119 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0954 0.0909 0.1826 n_refl.: 5176 remove outliers: r(all,work,free)=0.0950 0.0904 0.1826 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 0.3671 330.284 295.926 0.615 0.995 0.344 11.894-9.307 99.02 97 4 0.1748 525.643 511.140 0.951 0.999 0.340 9.237-7.194 100.00 213 7 0.1975 429.872 423.081 1.001 1.000 0.290 7.162-5.571 100.00 427 22 0.1841 322.566 314.149 0.975 1.001 0.274 5.546-4.326 100.00 867 58 0.0926 442.838 437.576 1.004 1.001 0.260 4.315-3.360 100.00 1859 96 0.0604 421.144 420.647 1.057 1.002 0.220 3.356-3.002 100.00 1373 60 0.0628 324.382 324.265 1.040 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9175 b_overall=-6.5501 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0904 r_free=0.1826 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0904 r_free=0.1826 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0904 r_free=0.1826 | n_water=224 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0914 r_free=0.1819 | n_water=221 | time (s): 18.570 (total time: 19.150) Filter (q & B) r_work=0.0987 r_free=0.1843 | n_water=218 | time (s): 1.350 (total time: 20.500) Compute maps r_work=0.0987 r_free=0.1843 | n_water=218 | time (s): 0.570 (total time: 21.070) Filter (map) r_work=0.1226 r_free=0.1936 | n_water=152 | time (s): 1.280 (total time: 22.350) Find peaks r_work=0.1226 r_free=0.1936 | n_water=152 | time (s): 0.480 (total time: 22.830) Add new water r_work=0.1528 r_free=0.2118 | n_water=219 | time (s): 1.420 (total time: 24.250) Refine new water occ: r_work=0.1022 r_free=0.1851 adp: r_work=0.1017 r_free=0.1857 occ: r_work=0.1009 r_free=0.1845 adp: r_work=0.1009 r_free=0.1851 occ: r_work=0.1003 r_free=0.1839 adp: r_work=0.1003 r_free=0.1839 ADP+occupancy (water only), MIN, final r_work=0.1003 r_free=0.1839 r_work=0.1003 r_free=0.1839 | n_water=219 | time (s): 10.380 (total time: 34.630) Filter (q & B) r_work=0.1003 r_free=0.1841 | n_water=217 | time (s): 1.660 (total time: 36.290) Filter (dist only) r_work=0.1013 r_free=0.1839 | n_water=215 | time (s): 16.350 (total time: 52.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.014308 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.224849 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 0.0907 0.1873 0.0966 0.011 1.0 3.8 0.5 0.6 0 0.507 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.07 18.73 9.66 6.943 17.723 0.225 5.053 8.85 18.76 9.91 8.126 17.855 0.225 4.990 Individual atomic B min max mean iso aniso Overall: 0.00 108.09 16.36 10.57 1742 0 Protein: 0.00 108.09 15.48 10.55 1519 0 Water: 0.00 54.01 22.09 N/A 215 0 Other: 13.70 47.65 29.22 N/A 8 0 Chain A: 0.00 108.09 15.97 N/A 1638 0 Chain S: 0.00 50.19 22.48 N/A 104 0 Histogram: Values Number of atoms 0.00 - 10.81 660 10.81 - 21.62 670 21.62 - 32.43 234 32.43 - 43.24 109 43.24 - 54.04 36 54.04 - 64.85 14 64.85 - 75.66 11 75.66 - 86.47 3 86.47 - 97.28 4 97.28 - 108.09 1 =========================== Idealize ADP of riding H ========================== r_work=0.0885 r_free=0.1876 r_work=0.0891 r_free=0.1877 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0891 r_free = 0.1877 target_work(ml) = 4.995 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1869 target_work(ml) = 4.987 | | 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.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1869 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.987499 | | target function (ml) not normalized (work): 24548.469383 | | target function (ml) not normalized (free): 2081.185315 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0930 0.0881 0.1869 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2113 0.2113 0.2239 n_refl.: 5174 remove outliers: r(all,work,free)=0.2113 0.2113 0.2239 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2113 0.2113 0.2239 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0930 0.0880 0.1870 n_refl.: 5174 remove outliers: r(all,work,free)=0.0930 0.0880 0.1870 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 0.3762 330.284 298.650 0.620 0.985 0.338 11.894-9.307 99.02 97 4 0.1838 525.643 509.187 0.954 0.990 0.330 9.237-7.194 100.00 213 7 0.2153 429.872 418.504 1.005 0.993 0.298 7.162-5.571 100.00 427 22 0.1945 322.566 314.640 0.988 0.995 0.283 5.546-4.326 100.00 867 58 0.0986 442.838 436.719 1.011 0.998 0.249 4.315-3.360 100.00 1859 96 0.0565 421.144 420.715 1.069 1.002 0.230 3.356-3.002 100.00 1373 60 0.0461 324.382 324.478 1.053 1.006 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.1680 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0880 r_free=0.1870 After: r_work=0.0883 r_free=0.1869 ================================== NQH flips ================================== r_work=0.0883 r_free=0.1869 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0885 r_free=0.1867 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0885 r_free=0.1867 | n_water=215 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0903 r_free=0.1867 | n_water=211 | time (s): 15.850 (total time: 16.360) Filter (q & B) r_work=0.0983 r_free=0.1827 | n_water=208 | time (s): 1.480 (total time: 17.840) Compute maps r_work=0.0983 r_free=0.1827 | n_water=208 | time (s): 0.560 (total time: 18.400) Filter (map) r_work=0.1200 r_free=0.1949 | n_water=161 | time (s): 1.310 (total time: 19.710) Find peaks r_work=0.1200 r_free=0.1949 | n_water=161 | time (s): 0.380 (total time: 20.090) Add new water r_work=0.1454 r_free=0.2102 | n_water=217 | time (s): 1.300 (total time: 21.390) Refine new water occ: r_work=0.0989 r_free=0.1863 adp: r_work=0.0980 r_free=0.1884 occ: r_work=0.0974 r_free=0.1873 adp: r_work=0.0974 r_free=0.1879 occ: r_work=0.0969 r_free=0.1868 adp: r_work=0.0968 r_free=0.1875 ADP+occupancy (water only), MIN, final r_work=0.0968 r_free=0.1875 r_work=0.0968 r_free=0.1875 | n_water=217 | time (s): 10.530 (total time: 31.920) Filter (q & B) r_work=0.0968 r_free=0.1875 | n_water=217 | time (s): 0.760 (total time: 32.680) Filter (dist only) r_work=0.0968 r_free=0.1875 | n_water=217 | time (s): 14.090 (total time: 46.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.998876 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.237756 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0909 0.1857 0.0948 0.011 1.2 7.0 0.5 0.6 0 0.499 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.09 18.57 9.48 8.050 18.191 0.238 5.002 8.94 18.60 9.66 9.090 18.341 0.238 4.952 Individual atomic B min max mean iso aniso Overall: 0.00 110.36 16.80 12.07 1744 0 Protein: 0.00 110.36 15.86 12.04 1519 0 Water: 0.00 54.89 22.94 N/A 217 0 Other: 12.78 51.50 28.55 N/A 8 0 Chain A: 0.00 110.36 16.33 N/A 1634 0 Chain S: 0.00 54.89 23.83 N/A 110 0 Histogram: Values Number of atoms 0.00 - 11.04 675 11.04 - 22.07 630 22.07 - 33.11 253 33.11 - 44.15 112 44.15 - 55.18 39 55.18 - 66.22 14 66.22 - 77.26 14 77.26 - 88.29 2 88.29 - 99.33 3 99.33 - 110.36 2 =========================== Idealize ADP of riding H ========================== r_work=0.0894 r_free=0.1860 r_work=0.0897 r_free=0.1859 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1859 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0891 r_free = 0.1850 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0891 r_free= 0.1850 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.952484 | | target function (ml) not normalized (work): 24376.128669 | | target function (ml) not normalized (free): 2295.372188 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1280 0.1830 5.556 6.1576| | 2: 3.78 - 3.00 1.00 2430 110 0.0417 0.1883 4.3336 12.918| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.36 1.00 0.98 13739.98| | 2: 3.78 - 3.00 2430 110 0.99 1.79 1.00 1.01 868.60| |alpha: min = 0.97 max = 1.01 mean = 1.00| |beta: min = 540.66 max = 22950.58 mean = 7385.36| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.95 mean = 7.14| |phase err.(test): min = 0.00 max = 89.63 mean = 7.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0939 0.0891 0.1850 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2152 0.2152 0.2270 n_refl.: 5174 remove outliers: r(all,work,free)=0.2152 0.2152 0.2270 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2152 0.2152 0.2270 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0890 0.1855 n_refl.: 5174 remove outliers: r(all,work,free)=0.0938 0.0890 0.1855 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 0.3852 330.284 301.078 0.637 0.985 0.359 11.894-9.307 99.02 97 4 0.1833 525.643 509.210 0.963 0.990 0.339 9.237-7.194 100.00 213 7 0.2242 429.872 416.550 0.999 0.994 0.303 7.162-5.571 100.00 427 22 0.2042 322.566 314.009 0.988 0.996 0.287 5.546-4.326 100.00 867 58 0.1034 442.838 436.654 1.014 0.998 0.245 4.315-3.360 100.00 1859 96 0.0578 421.144 421.205 1.082 1.002 0.230 3.356-3.002 100.00 1373 60 0.0388 324.382 324.647 1.068 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.7391 ================= 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 : 0.3622 0.2042 0.083 5.285 8.8 119.3 19.9 258 0.000 1_bss: 0.1561 0.1679 0.083 5.285 5.9 116.4 17.0 258 0.000 1_settarget: 0.1561 0.1679 0.083 5.285 5.9 116.4 17.0 258 0.000 1_nqh: 0.1561 0.1679 0.083 5.285 5.9 116.4 17.0 258 0.000 1_weight: 0.1561 0.1679 0.083 5.285 5.9 116.4 17.0 258 0.000 1_xyzrec: 0.1161 0.1784 0.010 0.986 5.9 116.4 17.0 258 0.202 1_adp: 0.1019 0.1778 0.010 0.986 2.2 111.4 17.3 258 0.202 1_regHadp: 0.1014 0.1783 0.010 0.986 2.2 111.4 17.3 258 0.202 1_occ: 0.1010 0.1782 0.010 0.986 2.2 111.4 17.3 258 0.202 2_bss: 0.1010 0.1780 0.010 0.986 1.2 110.4 16.4 258 0.202 2_settarget: 0.1010 0.1780 0.010 0.986 1.2 110.4 16.4 258 0.202 2_updatecdl: 0.1010 0.1780 0.010 1.006 1.2 110.4 16.4 258 0.202 2_nqh: 0.1010 0.1780 0.010 1.006 1.2 110.4 16.4 258 0.202 2_sol: 0.1133 0.1671 0.010 1.006 1.0 109.7 15.6 219 n/a 2_weight: 0.1133 0.1671 0.010 1.006 1.0 109.7 15.6 219 n/a 2_xyzrec: 0.1033 0.1740 0.009 0.940 1.0 109.7 15.6 219 n/a 2_adp: 0.0966 0.1802 0.009 0.940 0.0 107.5 16.4 219 n/a 2_regHadp: 0.0963 0.1807 0.009 0.940 0.0 107.5 16.4 219 n/a 2_occ: 0.0957 0.1798 0.009 0.940 0.0 107.5 16.4 219 n/a 3_bss: 0.0958 0.1807 0.009 0.940 0.0 107.5 16.4 219 n/a 3_settarget: 0.0958 0.1807 0.009 0.940 0.0 107.5 16.4 219 n/a 3_updatecdl: 0.0958 0.1807 0.009 0.945 0.0 107.5 16.4 219 n/a 3_nqh: 0.0957 0.1808 0.009 0.945 0.0 107.5 16.4 219 n/a 3_sol: 0.1069 0.1809 0.009 0.945 0.0 107.5 16.3 224 n/a 3_weight: 0.1069 0.1809 0.009 0.945 0.0 107.5 16.3 224 n/a 3_xyzrec: 0.0968 0.1815 0.011 1.039 0.0 107.5 16.3 224 n/a 3_adp: 0.0923 0.1842 0.011 1.039 0.0 107.7 16.3 224 n/a 3_regHadp: 0.0929 0.1855 0.011 1.039 0.0 107.7 16.3 224 n/a 3_occ: 0.0916 0.1837 0.011 1.039 0.0 107.7 16.3 224 n/a 4_bss: 0.0904 0.1826 0.011 1.039 0.0 107.7 16.3 224 n/a 4_settarget: 0.0904 0.1826 0.011 1.039 0.0 107.7 16.3 224 n/a 4_updatecdl: 0.0904 0.1826 0.011 1.046 0.0 107.7 16.3 224 n/a 4_nqh: 0.0904 0.1826 0.011 1.046 0.0 107.7 16.3 224 n/a 4_sol: 0.1013 0.1839 0.011 1.046 0.0 107.7 16.1 215 n/a 4_weight: 0.1013 0.1839 0.011 1.046 0.0 107.7 16.1 215 n/a 4_xyzrec: 0.0907 0.1873 0.011 1.027 0.0 107.7 16.1 215 n/a 4_adp: 0.0885 0.1876 0.011 1.027 0.0 108.1 16.4 215 n/a 4_regHadp: 0.0891 0.1877 0.011 1.027 0.0 108.1 16.4 215 n/a 4_occ: 0.0881 0.1869 0.011 1.027 0.0 108.1 16.4 215 n/a 5_bss: 0.0880 0.1870 0.011 1.027 0.0 108.1 16.4 215 n/a 5_settarget: 0.0880 0.1870 0.011 1.027 0.0 108.1 16.4 215 n/a 5_updatecdl: 0.0880 0.1870 0.011 1.033 0.0 108.1 16.4 215 n/a 5_setrh: 0.0883 0.1869 0.011 1.033 0.0 108.1 16.4 215 n/a 5_nqh: 0.0885 0.1867 0.011 1.033 0.0 108.1 16.4 215 n/a 5_sol: 0.0968 0.1875 0.011 1.033 0.0 108.1 16.5 217 n/a 5_weight: 0.0968 0.1875 0.011 1.033 0.0 108.1 16.5 217 n/a 5_xyzrec: 0.0909 0.1857 0.011 1.156 0.0 108.1 16.5 217 n/a 5_adp: 0.0894 0.1860 0.011 1.156 0.0 110.4 16.8 217 n/a 5_regHadp: 0.0897 0.1859 0.011 1.156 0.0 110.4 16.8 217 n/a 5_occ: 0.0891 0.1850 0.011 1.156 0.0 110.4 16.8 217 n/a end: 0.0890 0.1855 0.011 1.156 0.0 110.4 16.8 217 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8498250_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8498250_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2300 Refinement macro-cycles (run) : 471.2400 Write final files (write_after_run_outputs) : 10.4900 Total : 484.9600 Total CPU time: 8.48 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:49 PST -0800 (1735492729.58 s) Start R-work = 0.1561, R-free = 0.1679 Final R-work = 0.0890, R-free = 0.1855 =============================================================================== Job complete usr+sys time: 518.18 seconds wall clock time: 9 minutes 0.04 seconds (540.04 seconds total)