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_3025539.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_3025539.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3025539.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.28, per 1000 atoms: 0.38 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: 0.35 Conformation dependent library (CDL) restraints added in 203.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 578 0.92 - 1.18: 1086 1.18 - 1.43: 640 1.43 - 1.68: 822 1.68 - 1.94: 27 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " ideal model delta sigma weight residual 1.522 1.733 -0.211 1.14e-02 7.69e+03 3.42e+02 bond pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta sigma weight residual 1.447 1.643 -0.197 1.12e-02 7.97e+03 3.09e+02 bond pdb=" CA ALYS A 175 " pdb=" C ALYS A 175 " ideal model delta sigma weight residual 1.524 1.744 -0.221 1.27e-02 6.20e+03 3.02e+02 bond pdb=" N GLU A 84 " pdb=" CA GLU A 84 " ideal model delta sigma weight residual 1.456 1.685 -0.229 1.33e-02 5.65e+03 2.96e+02 bond pdb=" CA ILE A 21 " pdb=" C ILE A 21 " ideal model delta sigma weight residual 1.524 1.698 -0.173 1.05e-02 9.07e+03 2.72e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 3192 4.70 - 9.40: 1847 9.40 - 14.09: 621 14.09 - 18.79: 104 18.79 - 23.48: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 139.29 -16.69 1.00e+00 1.00e+00 2.79e+02 angle pdb=" O PHE A 162 " pdb=" C PHE A 162 " pdb=" N GLU A 163 " ideal model delta sigma weight residual 122.07 136.88 -14.81 1.03e+00 9.43e-01 2.07e+02 angle pdb=" O ALA A 179 " pdb=" C ALA A 179 " pdb=" N GLN A 180 " ideal model delta sigma weight residual 122.07 136.31 -14.24 1.03e+00 9.43e-01 1.91e+02 angle pdb=" O AGLU A 96 " pdb=" C AGLU A 96 " pdb=" N AASN A 97 " ideal model delta sigma weight residual 122.07 108.59 13.48 1.03e+00 9.43e-01 1.71e+02 angle pdb=" CD1 TYR A 141 " pdb=" CG TYR A 141 " pdb=" CD2 TYR A 141 " ideal model delta sigma weight residual 118.10 99.46 18.64 1.50e+00 4.44e-01 1.54e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.84: 1315 17.84 - 35.67: 118 35.67 - 53.50: 36 53.50 - 71.33: 11 71.33 - 89.16: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ASP A 60 " pdb=" N ASP A 60 " pdb=" CA ASP A 60 " pdb=" CB ASP A 60 " ideal model delta harmonic sigma weight residual -122.60 -142.88 20.28 0 2.50e+00 1.60e-01 6.58e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -142.58 19.98 0 2.50e+00 1.60e-01 6.39e+01 dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 140.72 -17.92 0 2.50e+00 1.60e-01 5.14e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.201: 107 0.201 - 0.401: 66 0.401 - 0.601: 44 0.601 - 0.800: 20 0.800 - 1.000: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.44 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CB VAL A 186 " pdb=" CA VAL A 186 " pdb=" CG1 VAL A 186 " pdb=" CG2 VAL A 186 " both_signs ideal model delta sigma weight residual False -2.63 -3.59 0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.042 2.00e-02 2.50e+03 7.73e-02 1.79e+02 pdb=" CG PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.111 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.153 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.083 2.00e-02 2.50e+03 5.37e-02 8.66e+01 pdb=" CG BTYR A 67 " -0.084 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.032 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.025 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.044 2.00e-02 2.50e+03 5.27e-02 8.34e+01 pdb=" CG TYR A 141 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.114 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.066 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.009 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1099 2.33 - 2.90: 8192 2.90 - 3.47: 10526 3.47 - 4.03: 15223 4.03 - 4.60: 21520 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.764 2.100 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.767 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.818 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.824 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.831 2.450 ... (remaining 56555 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_3025539_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= 0.3605 r_free= 0.2058 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468562 | | target function (ml) not normalized (work): 22030.008575 | | target function (ml) not normalized (free): 1148.860852 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3783 0.2261 4.8508 4.9152| | 2: 3.78 - 3.00 1.00 2430 110 0.3387 0.1716 4.0753 4.0991| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.91 0.83 0.13 6618.52| | 2: 3.78 - 3.00 2430 110 0.94 11.24 1.48 0.26 446.88| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 377.15 max = 12082.63 mean = 3576.51| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.34| |phase err.(test): min = 0.00 max = 89.97 mean = 33.54| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.229 1557 Z= 5.385 Angle : 5.286 18.642 2118 Z= 3.693 Chirality : 0.363 1.000 243 Planarity : 0.034 0.118 284 Dihedral : 13.779 89.165 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 28.65 % 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: -2.56 (0.47), residues: 224 helix: -2.53 (0.38), residues: 109 sheet: -1.12 (0.81), residues: 28 loop : -0.37 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.015 ARG A 28 TYR 0.101 0.033 TYR A 141 PHE 0.107 0.047 PHE A 164 HIS 0.062 0.021 HIS A 138 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= 0.3605 r_free= 0.2058 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468562 | | target function (ml) not normalized (work): 22030.008575 | | target function (ml) not normalized (free): 1148.860852 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3562 0.3638 0.2146 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3562 0.3638 0.2146 n_refl.: 5182 remove outliers: r(all,work,free)=0.2512 0.2535 0.2146 n_refl.: 5178 overall B=-2.86 to atoms: r(all,work,free)=0.2403 0.2422 0.2098 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1563 0.1562 0.1597 n_refl.: 5178 remove outliers: r(all,work,free)=0.1559 0.1557 0.1597 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 0.3825 449.899 407.851 0.647 1.081 0.392 11.894-9.307 99.02 97 4 0.1860 714.700 695.608 0.934 1.077 0.372 9.237-7.194 100.00 213 7 0.2222 584.483 575.157 0.965 1.069 0.358 7.162-5.571 100.00 427 22 0.2285 438.583 424.668 0.929 1.054 0.308 5.546-4.326 100.00 867 58 0.1376 602.113 595.153 0.974 1.029 0.231 4.315-3.360 100.00 1859 96 0.1317 572.616 566.197 1.057 0.988 0.200 3.356-3.002 100.00 1373 60 0.1591 441.053 434.467 1.077 0.947 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6520 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1557 r_free=0.1597 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN Total number of N/Q/H flips: 1 r_work=0.1557 r_free=0.1596 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.942803 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.550799 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 0.1157 0.1757 0.0600 0.010 1.0 1.9 0.5 0.0 0 9.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 17.57 6.00 3.013 16.002 1.551 0.018 10.20 17.60 7.39 4.587 16.181 1.551 0.015 Individual atomic B min max mean iso aniso Overall: 2.51 111.44 17.37 4.98 1785 0 Protein: 2.51 111.30 14.69 4.98 1519 0 Water: 4.01 111.44 32.95 N/A 258 0 Other: 17.26 33.99 23.38 N/A 8 0 Chain A: 2.51 111.44 17.37 N/A 1785 0 Histogram: Values Number of atoms 2.51 - 13.41 952 13.41 - 24.30 461 24.30 - 35.19 185 35.19 - 46.09 105 46.09 - 56.98 52 56.98 - 67.87 14 67.87 - 78.76 7 78.76 - 89.66 5 89.66 - 100.55 1 100.55 - 111.44 3 =========================== Idealize ADP of riding H ========================== r_work=0.1020 r_free=0.1760 r_work=0.1014 r_free=0.1765 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1014 r_free = 0.1765 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 = 0.1009 r_free = 0.1749 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.24 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= 0.1009 r_free= 0.1749 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013912 | | target function (ls_wunit_k1) not normalized (work): 68.503114 | | target function (ls_wunit_k1) not normalized (free): 10.091037 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1047 0.1009 0.1749 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2085 0.2084 0.2215 n_refl.: 5176 remove outliers: r(all,work,free)=0.2085 0.2084 0.2215 n_refl.: 5176 overall B=-0.93 to atoms: r(all,work,free)=0.2047 0.2044 0.2204 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1053 0.1015 0.1761 n_refl.: 5176 remove outliers: r(all,work,free)=0.1053 0.1015 0.1761 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 0.3269 330.435 313.912 0.672 1.017 0.381 11.894-9.307 99.02 97 4 0.1493 524.922 517.071 0.979 1.018 0.361 9.237-7.194 100.00 213 7 0.1681 429.282 430.135 1.017 1.016 0.320 7.162-5.571 100.00 427 22 0.1610 322.124 319.588 0.976 1.012 0.302 5.546-4.326 100.00 867 58 0.0917 442.230 439.565 0.991 1.006 0.208 4.315-3.360 100.00 1859 96 0.0768 420.566 420.508 1.042 0.996 0.197 3.356-3.002 100.00 1373 60 0.1010 323.938 322.310 1.021 0.987 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3370 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1015 r_free=0.1761 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN Total number of N/Q/H flips: 1 r_work=0.1017 r_free=0.1759 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1017 r_free=0.1759 | n_water=258 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.1057 r_free=0.1752 | n_water=245 | time (s): 19.380 (total time: 19.840) Filter (q & B) r_work=0.1058 r_free=0.1757 | n_water=242 | time (s): 1.450 (total time: 21.290) Compute maps r_work=0.1058 r_free=0.1757 | n_water=242 | time (s): 0.530 (total time: 21.820) Filter (map) r_work=0.1371 r_free=0.1815 | n_water=138 | time (s): 1.490 (total time: 23.310) Find peaks r_work=0.1371 r_free=0.1815 | n_water=138 | time (s): 0.600 (total time: 23.910) Add new water r_work=0.1749 r_free=0.2101 | n_water=232 | time (s): 1.400 (total time: 25.310) Refine new water occ: r_work=0.1161 r_free=0.1657 adp: r_work=0.1134 r_free=0.1667 occ: r_work=0.1130 r_free=0.1640 adp: r_work=0.1117 r_free=0.1648 occ: r_work=0.1116 r_free=0.1637 adp: r_work=0.1116 r_free=0.1637 ADP+occupancy (water only), MIN, final r_work=0.1116 r_free=0.1637 r_work=0.1116 r_free=0.1637 | n_water=232 | time (s): 5.660 (total time: 30.970) Filter (q & B) r_work=0.1116 r_free=0.1637 | n_water=232 | time (s): 0.980 (total time: 31.950) Filter (dist only) r_work=0.1125 r_free=0.1646 | n_water=227 | time (s): 18.010 (total time: 49.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.942767 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.871323 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 0.1026 0.1714 0.0688 0.009 1.0 5.1 0.5 0.6 0 10.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.26 17.14 6.88 4.475 16.654 2.871 0.014 9.50 17.25 7.75 5.430 16.980 2.871 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.01 16.29 6.41 1754 0 Protein: 0.00 107.01 14.83 6.39 1519 0 Water: 0.00 62.79 25.71 N/A 227 0 Other: 11.74 37.53 24.48 N/A 8 0 Chain A: 0.00 107.01 15.51 N/A 1661 0 Chain S: 1.29 55.00 30.16 N/A 93 0 Histogram: Values Number of atoms 0.00 - 10.70 703 10.70 - 21.40 652 21.40 - 32.10 202 32.10 - 42.80 123 42.80 - 53.51 38 53.51 - 64.21 23 64.21 - 74.91 6 74.91 - 85.61 3 85.61 - 96.31 2 96.31 - 107.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.0950 r_free=0.1725 r_work=0.0947 r_free=0.1727 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0947 r_free = 0.1727 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0949 r_free = 0.1700 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.18 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= 0.0949 r_free= 0.1700 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012282 | | target function (ls_wunit_k1) not normalized (work): 60.474846 | | target function (ls_wunit_k1) not normalized (free): 8.967604 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0988 0.0949 0.1700 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2120 0.2126 0.2112 n_refl.: 5176 remove outliers: r(all,work,free)=0.2120 0.2126 0.2112 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2120 0.2126 0.2112 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0991 0.0953 0.1707 n_refl.: 5176 remove outliers: r(all,work,free)=0.0987 0.0948 0.1707 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 0.3212 329.831 309.225 0.658 1.007 0.360 11.894-9.307 99.02 97 4 0.1488 524.922 518.672 0.983 1.009 0.347 9.237-7.194 100.00 213 7 0.1500 429.282 429.942 1.020 1.008 0.315 7.162-5.571 100.00 427 22 0.1408 322.124 320.123 0.995 1.007 0.310 5.546-4.326 100.00 867 58 0.0795 442.230 439.993 1.006 1.004 0.250 4.315-3.360 100.00 1859 96 0.0738 420.566 420.484 1.052 1.000 0.200 3.356-3.002 100.00 1373 60 0.0987 323.938 322.659 1.025 0.995 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9557 b_overall=-3.9543 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0948 r_free=0.1707 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0950 r_free=0.1709 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0950 r_free=0.1709 | n_water=227 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0962 r_free=0.1703 | n_water=224 | time (s): 18.370 (total time: 18.930) Filter (q & B) r_work=0.1047 r_free=0.1683 | n_water=221 | time (s): 1.530 (total time: 20.460) Compute maps r_work=0.1047 r_free=0.1683 | n_water=221 | time (s): 0.470 (total time: 20.930) Filter (map) r_work=0.1280 r_free=0.1800 | n_water=153 | time (s): 1.330 (total time: 22.260) Find peaks r_work=0.1280 r_free=0.1800 | n_water=153 | time (s): 0.390 (total time: 22.650) Add new water r_work=0.1646 r_free=0.2097 | n_water=234 | time (s): 1.450 (total time: 24.100) Refine new water occ: r_work=0.1068 r_free=0.1617 adp: r_work=0.1060 r_free=0.1643 occ: r_work=0.1050 r_free=0.1618 adp: r_work=0.1049 r_free=0.1634 occ: r_work=0.1040 r_free=0.1611 adp: r_work=0.1039 r_free=0.1624 ADP+occupancy (water only), MIN, final r_work=0.1039 r_free=0.1624 r_work=0.1039 r_free=0.1624 | n_water=234 | time (s): 11.500 (total time: 35.600) Filter (q & B) r_work=0.1040 r_free=0.1630 | n_water=232 | time (s): 1.500 (total time: 37.100) Filter (dist only) r_work=0.1050 r_free=0.1642 | n_water=230 | time (s): 18.600 (total time: 55.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.100062 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.192870 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 0.0948 0.1753 0.0805 0.011 1.1 4.8 0.5 0.6 0 0.550 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.48 17.53 8.05 5.360 17.630 0.193 5.174 9.05 17.73 8.68 6.802 17.609 0.193 5.085 Individual atomic B min max mean iso aniso Overall: 0.00 106.72 16.16 8.34 1757 0 Protein: 0.00 106.72 14.88 8.34 1519 0 Water: 0.00 59.31 24.35 N/A 230 0 Other: 13.03 40.30 25.49 N/A 8 0 Chain A: 0.00 106.72 15.55 N/A 1651 0 Chain S: 0.00 59.31 25.72 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.67 700 10.67 - 21.34 650 21.34 - 32.01 216 32.01 - 42.69 116 42.69 - 53.36 41 53.36 - 64.03 17 64.03 - 74.70 9 74.70 - 85.37 3 85.37 - 96.04 3 96.04 - 106.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.0905 r_free=0.1773 r_work=0.0910 r_free=0.1782 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0910 r_free = 0.1782 target_work(ml) = 5.087 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0900 r_free = 0.1774 target_work(ml) = 5.079 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0900 r_free= 0.1774 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.079377 | | target function (ml) not normalized (work): 25000.692969 | | target function (ml) not normalized (free): 1742.529635 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0945 0.0900 0.1774 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2032 0.2038 0.2049 n_refl.: 5174 remove outliers: r(all,work,free)=0.2032 0.2038 0.2049 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2032 0.2038 0.2049 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0889 0.1769 n_refl.: 5174 remove outliers: r(all,work,free)=0.0934 0.0889 0.1769 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 0.3570 329.831 304.316 0.581 0.991 0.319 11.894-9.307 99.02 97 4 0.1870 524.922 509.022 0.947 0.996 0.318 9.237-7.194 100.00 213 7 0.1886 429.282 421.491 1.008 0.998 0.310 7.162-5.571 100.00 427 22 0.1811 322.124 314.155 0.980 0.999 0.310 5.546-4.326 100.00 867 58 0.0897 442.230 437.467 0.997 1.001 0.240 4.315-3.360 100.00 1859 96 0.0591 420.566 419.847 1.050 1.003 0.230 3.356-3.002 100.00 1373 60 0.0633 323.938 323.795 1.025 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.1186 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0889 r_free=0.1770 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=0.0889 r_free=0.1770 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0889 r_free=0.1770 | n_water=230 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.0907 r_free=0.1766 | n_water=226 | time (s): 20.220 (total time: 20.910) Filter (q & B) r_work=0.0954 r_free=0.1793 | n_water=223 | time (s): 1.530 (total time: 22.440) Compute maps r_work=0.0954 r_free=0.1793 | n_water=223 | time (s): 0.590 (total time: 23.030) Filter (map) r_work=0.1209 r_free=0.1899 | n_water=157 | time (s): 1.920 (total time: 24.950) Find peaks r_work=0.1209 r_free=0.1899 | n_water=157 | time (s): 0.480 (total time: 25.430) Add new water r_work=0.1556 r_free=0.2131 | n_water=233 | time (s): 1.440 (total time: 26.870) Refine new water occ: r_work=0.1010 r_free=0.1792 adp: r_work=0.1006 r_free=0.1798 occ: r_work=0.0996 r_free=0.1785 adp: r_work=0.0996 r_free=0.1792 occ: r_work=0.0986 r_free=0.1778 adp: r_work=0.0985 r_free=0.1786 ADP+occupancy (water only), MIN, final r_work=0.0985 r_free=0.1786 r_work=0.0985 r_free=0.1786 | n_water=233 | time (s): 9.350 (total time: 36.220) Filter (q & B) r_work=0.0985 r_free=0.1784 | n_water=232 | time (s): 1.520 (total time: 37.740) Filter (dist only) r_work=0.0993 r_free=0.1771 | n_water=230 | time (s): 18.700 (total time: 56.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.015247 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.247965 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 0.1817 0.0907 0.011 1.0 4.5 0.5 0.0 0 0.508 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.10 18.17 9.07 6.567 17.684 0.248 5.052 8.83 18.50 9.67 8.136 17.824 0.248 4.984 Individual atomic B min max mean iso aniso Overall: 0.00 106.56 16.51 10.56 1757 0 Protein: 0.00 106.56 15.34 10.54 1519 0 Water: 0.00 54.31 23.90 N/A 230 0 Other: 12.55 43.19 26.51 N/A 8 0 Chain A: 0.00 106.56 15.91 N/A 1641 0 Chain S: 0.00 54.31 25.02 N/A 116 0 Histogram: Values Number of atoms 0.00 - 10.66 685 10.66 - 21.31 636 21.31 - 31.97 239 31.97 - 42.62 112 42.62 - 53.28 49 53.28 - 63.93 19 63.93 - 74.59 4 74.59 - 85.25 9 85.25 - 95.90 2 95.90 - 106.56 2 =========================== Idealize ADP of riding H ========================== r_work=0.0883 r_free=0.1850 r_work=0.0888 r_free=0.1856 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0888 r_free = 0.1856 target_work(ml) = 4.990 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0877 r_free = 0.1836 target_work(ml) = 4.982 | | occupancies: max = 1.00 min = 0.18 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= 0.0877 r_free= 0.1836 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.982424 | | target function (ml) not normalized (work): 24523.489726 | | target function (ml) not normalized (free): 2025.646063 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0926 0.0877 0.1836 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2071 0.2073 0.2188 n_refl.: 5174 remove outliers: r(all,work,free)=0.2071 0.2073 0.2188 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2071 0.2073 0.2188 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0926 0.0878 0.1846 n_refl.: 5174 remove outliers: r(all,work,free)=0.0926 0.0878 0.1846 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 0.3829 329.831 300.007 0.579 0.990 0.318 11.894-9.307 99.02 97 4 0.1981 524.922 506.818 0.944 0.996 0.317 9.237-7.194 100.00 213 7 0.2087 429.282 419.627 1.005 0.999 0.295 7.162-5.571 100.00 427 22 0.1988 322.124 312.991 0.987 1.000 0.290 5.546-4.326 100.00 867 58 0.0939 442.230 437.377 1.006 1.001 0.250 4.315-3.360 100.00 1859 96 0.0563 420.566 419.831 1.065 1.002 0.230 3.356-3.002 100.00 1373 60 0.0472 323.938 323.409 1.044 1.003 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.8528 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0877 r_free=0.1846 After: r_work=0.0880 r_free=0.1844 ================================== NQH flips ================================== r_work=0.0880 r_free=0.1844 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0880 r_free=0.1844 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0880 r_free=0.1844 | n_water=230 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0898 r_free=0.1857 | n_water=226 | time (s): 17.410 (total time: 17.950) Filter (q & B) r_work=0.0998 r_free=0.1859 | n_water=223 | time (s): 1.230 (total time: 19.180) Compute maps r_work=0.0998 r_free=0.1859 | n_water=223 | time (s): 0.420 (total time: 19.600) Filter (map) r_work=0.1254 r_free=0.1956 | n_water=162 | time (s): 1.630 (total time: 21.230) Find peaks r_work=0.1254 r_free=0.1956 | n_water=162 | time (s): 0.520 (total time: 21.750) Add new water r_work=0.1553 r_free=0.2207 | n_water=231 | time (s): 1.420 (total time: 23.170) Refine new water occ: r_work=0.0991 r_free=0.1895 adp: r_work=0.0982 r_free=0.1902 occ: r_work=0.0975 r_free=0.1886 adp: r_work=0.0975 r_free=0.1886 occ: r_work=0.0975 r_free=0.1886 adp: r_work=0.0975 r_free=0.1886 ADP+occupancy (water only), MIN, final r_work=0.0975 r_free=0.1886 r_work=0.0975 r_free=0.1886 | n_water=231 | time (s): 10.010 (total time: 33.180) Filter (q & B) r_work=0.0975 r_free=0.1889 | n_water=230 | time (s): 1.350 (total time: 34.530) Filter (dist only) r_work=0.0978 r_free=0.1898 | n_water=229 | time (s): 18.240 (total time: 52.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.946630 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.203855 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 0.0917 0.1896 0.0978 0.011 1.1 7.7 0.5 0.0 0 0.473 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.17 18.96 9.78 8.034 18.020 0.204 5.019 8.97 18.92 9.95 8.840 18.146 0.204 4.965 Individual atomic B min max mean iso aniso Overall: 0.00 105.58 16.64 11.69 1756 0 Protein: 0.00 105.58 15.74 11.66 1519 0 Water: 0.00 54.07 22.30 N/A 229 0 Other: 10.83 46.72 26.80 N/A 8 0 Chain A: 0.00 105.58 16.19 N/A 1636 0 Chain S: 0.00 53.31 22.77 N/A 120 0 Histogram: Values Number of atoms 0.00 - 10.56 660 10.56 - 21.12 632 21.12 - 31.67 273 31.67 - 42.23 106 42.23 - 52.79 43 52.79 - 63.35 19 63.35 - 73.90 10 73.90 - 84.46 6 84.46 - 95.02 5 95.02 - 105.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.0897 r_free=0.1892 r_work=0.0900 r_free=0.1891 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0900 r_free = 0.1891 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0892 r_free = 0.1882 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0892 r_free= 0.1882 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.965191 | | target function (ml) not normalized (work): 24438.671820 | | target function (ml) not normalized (free): 2167.571638 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1266 0.1867 5.5401 6.1973| | 2: 3.78 - 3.00 1.00 2430 110 0.0436 0.1907 4.3757 11.705| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.49 1.00 0.98 13813.48| | 2: 3.78 - 3.00 2430 110 0.99 1.97 1.00 1.01 942.25| |alpha: min = 0.97 max = 1.01 mean = 0.99| |beta: min = 606.25 max = 23295.60 mean = 7458.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.96 mean = 7.30| |phase err.(test): min = 0.00 max = 81.32 mean = 7.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0942 0.0892 0.1882 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2113 0.2117 0.2181 n_refl.: 5174 remove outliers: r(all,work,free)=0.2113 0.2117 0.2181 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2113 0.2117 0.2181 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0941 0.0892 0.1887 n_refl.: 5174 remove outliers: r(all,work,free)=0.0941 0.0892 0.1887 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 0.3997 329.831 298.955 0.576 0.986 0.318 11.894-9.307 99.02 97 4 0.2040 524.922 506.653 0.954 0.993 0.317 9.237-7.194 100.00 213 7 0.2235 429.282 417.024 1.002 0.997 0.303 7.162-5.571 100.00 427 22 0.2052 322.124 313.064 0.993 0.999 0.299 5.546-4.326 100.00 867 58 0.0985 442.230 436.260 1.017 1.001 0.250 4.315-3.360 100.00 1859 96 0.0568 420.566 420.180 1.085 1.003 0.240 3.356-3.002 100.00 1373 60 0.0418 323.938 323.867 1.063 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.7216 ================= 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 : 0.3605 0.2058 0.081 5.286 8.8 119.3 19.9 258 0.000 1_bss: 0.1557 0.1597 0.081 5.286 6.0 116.4 17.0 258 0.000 1_settarget: 0.1557 0.1597 0.081 5.286 6.0 116.4 17.0 258 0.000 1_nqh: 0.1557 0.1596 0.081 5.286 6.0 116.4 17.0 258 0.003 1_weight: 0.1557 0.1596 0.081 5.286 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1157 0.1757 0.010 0.996 6.0 116.4 17.0 258 0.200 1_adp: 0.1020 0.1760 0.010 0.996 2.5 111.4 17.4 258 0.200 1_regHadp: 0.1014 0.1765 0.010 0.996 2.5 111.4 17.4 258 0.200 1_occ: 0.1009 0.1749 0.010 0.996 2.5 111.4 17.4 258 0.200 2_bss: 0.1015 0.1761 0.010 0.996 1.6 110.5 16.4 258 0.200 2_settarget: 0.1015 0.1761 0.010 0.996 1.6 110.5 16.4 258 0.200 2_updatecdl: 0.1015 0.1761 0.010 1.022 1.6 110.5 16.4 258 0.200 2_nqh: 0.1017 0.1759 0.010 1.022 1.6 110.5 16.4 258 0.197 2_sol: 0.1125 0.1646 0.010 1.022 1.0 110.4 15.7 227 n/a 2_weight: 0.1125 0.1646 0.010 1.022 1.0 110.4 15.7 227 n/a 2_xyzrec: 0.1026 0.1714 0.009 0.958 1.0 110.4 15.7 227 n/a 2_adp: 0.0950 0.1725 0.009 0.958 0.0 107.0 16.3 227 n/a 2_regHadp: 0.0947 0.1727 0.009 0.958 0.0 107.0 16.3 227 n/a 2_occ: 0.0949 0.1700 0.009 0.958 0.0 107.0 16.3 227 n/a 3_bss: 0.0948 0.1707 0.009 0.958 0.0 107.0 16.3 227 n/a 3_settarget: 0.0948 0.1707 0.009 0.958 0.0 107.0 16.3 227 n/a 3_updatecdl: 0.0948 0.1707 0.009 0.963 0.0 107.0 16.3 227 n/a 3_nqh: 0.0950 0.1709 0.009 0.963 0.0 107.0 16.3 227 n/a 3_sol: 0.1050 0.1642 0.009 0.963 0.0 107.0 16.2 230 n/a 3_weight: 0.1050 0.1642 0.009 0.963 0.0 107.0 16.2 230 n/a 3_xyzrec: 0.0948 0.1753 0.011 1.061 0.0 107.0 16.2 230 n/a 3_adp: 0.0905 0.1773 0.011 1.061 0.0 106.7 16.2 230 n/a 3_regHadp: 0.0910 0.1782 0.011 1.061 0.0 106.7 16.2 230 n/a 3_occ: 0.0900 0.1774 0.011 1.061 0.0 106.7 16.2 230 n/a 4_bss: 0.0889 0.1770 0.011 1.061 0.0 106.7 16.2 230 n/a 4_settarget: 0.0889 0.1770 0.011 1.061 0.0 106.7 16.2 230 n/a 4_updatecdl: 0.0889 0.1770 0.011 1.079 0.0 106.7 16.2 230 n/a 4_nqh: 0.0889 0.1770 0.011 1.079 0.0 106.7 16.2 230 n/a 4_sol: 0.0993 0.1771 0.011 1.079 0.0 106.7 16.2 230 n/a 4_weight: 0.0993 0.1771 0.011 1.079 0.0 106.7 16.2 230 n/a 4_xyzrec: 0.0910 0.1817 0.011 1.035 0.0 106.7 16.2 230 n/a 4_adp: 0.0883 0.1850 0.011 1.035 0.0 106.6 16.5 230 n/a 4_regHadp: 0.0888 0.1856 0.011 1.035 0.0 106.6 16.5 230 n/a 4_occ: 0.0877 0.1836 0.011 1.035 0.0 106.6 16.5 230 n/a 5_bss: 0.0877 0.1846 0.011 1.035 0.0 106.6 16.5 230 n/a 5_settarget: 0.0877 0.1846 0.011 1.035 0.0 106.6 16.5 230 n/a 5_updatecdl: 0.0877 0.1846 0.011 1.042 0.0 106.6 16.5 230 n/a 5_setrh: 0.0880 0.1844 0.011 1.042 0.0 106.6 16.5 230 n/a 5_nqh: 0.0880 0.1844 0.011 1.042 0.0 106.6 16.5 230 n/a 5_sol: 0.0978 0.1898 0.011 1.042 0.0 106.6 16.4 229 n/a 5_weight: 0.0978 0.1898 0.011 1.042 0.0 106.6 16.4 229 n/a 5_xyzrec: 0.0917 0.1896 0.011 1.081 0.0 106.6 16.4 229 n/a 5_adp: 0.0897 0.1892 0.011 1.081 0.0 105.6 16.6 229 n/a 5_regHadp: 0.0900 0.1891 0.011 1.081 0.0 105.6 16.6 229 n/a 5_occ: 0.0892 0.1882 0.011 1.081 0.0 105.6 16.6 229 n/a end: 0.0892 0.1887 0.011 1.081 0.0 105.6 16.6 229 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3025539_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3025539_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.2500 Refinement macro-cycles (run) : 484.9700 Write final files (write_after_run_outputs) : 9.7700 Total : 498.9900 Total CPU time: 8.72 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:04 PST -0800 (1735492744.15 s) Start R-work = 0.1557, R-free = 0.1597 Final R-work = 0.0892, R-free = 0.1887 =============================================================================== Job complete usr+sys time: 530.41 seconds wall clock time: 9 minutes 12.57 seconds (552.57 seconds total)