Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7766834.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7766834.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7766834.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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.00, per 1000 atoms: 0.59 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: 0.51 Conformation dependent library (CDL) restraints added in 150.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.90: 429 0.90 - 1.17: 1199 1.17 - 1.43: 682 1.43 - 1.70: 820 1.70 - 1.97: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" N THR A 125 " pdb=" CA THR A 125 " ideal model delta sigma weight residual 1.456 1.671 -0.215 1.16e-02 7.43e+03 3.43e+02 bond pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 1.460 1.675 -0.216 1.21e-02 6.83e+03 3.18e+02 bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.252 0.207 1.20e-02 6.94e+03 2.98e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.490 -0.169 1.00e-02 1.00e+04 2.85e+02 bond pdb=" C VAL A 25 " pdb=" O VAL A 25 " ideal model delta sigma weight residual 1.237 1.422 -0.185 1.12e-02 7.97e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 2988 4.38 - 8.76: 1875 8.76 - 13.14: 725 13.14 - 17.52: 160 17.52 - 21.91: 29 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 133.45 -14.25 9.00e-01 1.23e+00 2.51e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 133.77 -12.54 8.10e-01 1.52e+00 2.40e+02 angle pdb=" O VAL A 177 " pdb=" C VAL A 177 " pdb=" N ALA A 178 " ideal model delta sigma weight residual 121.94 136.04 -14.10 1.00e+00 1.00e+00 1.99e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 106.74 12.46 9.00e-01 1.23e+00 1.92e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 110.61 8.68 6.50e-01 2.37e+00 1.78e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.66: 1323 17.66 - 35.30: 105 35.30 - 52.95: 38 52.95 - 70.60: 11 70.60 - 88.25: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N SER A 47 " pdb=" C SER A 47 " pdb=" CA SER A 47 " pdb=" CB SER A 47 " ideal model delta harmonic sigma weight residual 122.80 140.21 -17.41 0 2.50e+00 1.60e-01 4.85e+01 dihedral pdb=" C SER A 47 " pdb=" N SER A 47 " pdb=" CA SER A 47 " pdb=" CB SER A 47 " ideal model delta harmonic sigma weight residual -122.60 -139.63 17.03 0 2.50e+00 1.60e-01 4.64e+01 dihedral pdb=" C ILE A 21 " pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual -122.00 -138.83 16.83 0 2.50e+00 1.60e-01 4.53e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 85 0.182 - 0.363: 73 0.363 - 0.544: 45 0.544 - 0.726: 33 0.726 - 0.907: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -3.50 0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.69 -0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" CA SER A 47 " pdb=" N SER A 47 " pdb=" C SER A 47 " pdb=" CB SER A 47 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.87e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.118 2.00e-02 2.50e+03 7.88e-02 1.86e+02 pdb=" CG PHE A 119 " -0.125 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.094 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.124 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.072 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.032 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.138 2.00e-02 2.50e+03 7.86e-02 1.85e+02 pdb=" CG PHE A 164 " 0.165 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.089 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 123 " -0.040 2.00e-02 2.50e+03 9.05e-02 8.19e+01 pdb=" C VAL A 123 " 0.156 2.00e-02 2.50e+03 pdb=" O VAL A 123 " -0.064 2.00e-02 2.50e+03 pdb=" N THR A 124 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 700 2.26 - 2.85: 7720 2.85 - 3.43: 10601 3.43 - 4.02: 15338 4.02 - 4.60: 22374 Nonbonded interactions: 56733 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.677 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.827 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HA3BGLY A 65 " pdb=" HA BPRO A 66 " model vdw 1.830 2.440 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.832 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.849 2.100 ... (remaining 56728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_7766834_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2785 r_free= 0.1771 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.402822 | | target function (ml) not normalized (work): 71515.031553 | | target function (ml) not normalized (free): 3245.044172 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3214 0.2068 7.6189 5.0206| | 2: 3.63 - 2.88 1.00 2711 122 0.2631 0.1714 4.3229 4.3237| | 3: 2.88 - 2.52 1.00 2682 148 0.2548 0.1620 4.1756 4.1665| | 4: 2.52 - 2.29 1.00 2661 139 0.2539 0.1455 3.4861 3.4696| | 5: 2.29 - 2.13 1.00 2678 122 0.2635 0.1473 3.3715 3.4408| | 6: 2.13 - 2.00 1.00 2692 117 0.2731 0.1913 3.274 3.4237| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.64 2819 159 0.88 17.37 0.77 0.23 1273.67| | 2: 3.63 - 2.88 2711 122 0.83 23.50 1.31 0.23 1273.67| | 3: 2.88 - 2.52 2682 148 0.74 32.52 1.29 0.23 1273.67| | 4: 2.52 - 2.29 2661 139 0.94 10.42 1.30 0.26 118.39| | 5: 2.29 - 2.13 2678 122 0.93 12.46 1.31 0.26 118.39| | 6: 2.13 - 2.00 2692 117 0.91 15.08 1.33 0.26 118.39| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 118.39 max = 1273.67 mean = 702.47| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.94 mean = 18.57| |phase err.(test): min = 0.00 max = 88.54 mean = 18.69| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.241 1557 Z= 5.449 Angle : 5.364 17.071 2118 Z= 3.752 Chirality : 0.368 0.907 243 Planarity : 0.031 0.104 284 Dihedral : 14.050 88.249 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 34.05 % 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: -2.21 (0.50), residues: 224 helix: -2.64 (0.36), residues: 109 sheet: -0.60 (0.93), residues: 28 loop : 0.28 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.016 ARG A 28 TYR 0.074 0.023 TYR A 139 PHE 0.168 0.053 PHE A 164 HIS 0.084 0.036 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2785 r_free= 0.1771 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.402822 | | target function (ml) not normalized (work): 71515.031553 | | target function (ml) not normalized (free): 3245.044172 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3193 percent. r_work = 0.2917 r_free = 0.1959 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2863 0.2917 0.1959 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2863 0.2917 0.1959 n_refl.: 17050 remove outliers: r(all,work,free)=0.2151 0.2162 0.1959 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2124 0.2135 0.1943 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1614 0.1612 0.1663 n_refl.: 17045 remove outliers: r(all,work,free)=0.1612 0.1610 0.1663 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.4083 391.314 357.986 0.636 1.013 0.380 11.894-9.307 99.02 97 4 0.1840 633.478 613.736 0.929 1.013 0.380 9.237-7.194 100.00 213 7 0.2196 518.121 509.487 0.955 1.013 0.380 7.162-5.571 100.00 427 22 0.2333 388.851 377.478 0.925 1.012 0.289 5.546-4.326 100.00 867 58 0.1385 533.829 527.335 0.962 1.010 0.225 4.315-3.360 100.00 1859 96 0.1311 507.677 503.867 1.017 1.006 0.201 3.356-2.611 100.00 3867 181 0.1664 333.515 329.196 1.012 1.000 0.034 2.608-2.000 99.99 8818 434 0.1626 217.394 213.362 1.028 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4380 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1610 r_free=0.1663 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1613 r_free=0.1663 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.084498 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.896632 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1352 0.1640 0.0288 0.009 1.0 1.0 0.5 0.0 0 11.542 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.40 2.88 3.013 18.455 0.897 0.023 12.78 16.68 3.90 3.623 18.685 0.897 0.020 Individual atomic B min max mean iso aniso Overall: 6.04 113.90 19.92 4.11 1785 0 Protein: 6.04 113.27 17.15 4.11 1519 0 Water: 8.42 113.90 36.01 N/A 258 0 Other: 21.33 37.76 26.41 N/A 8 0 Chain A: 6.04 113.90 19.92 N/A 1785 0 Histogram: Values Number of atoms 6.04 - 16.83 1078 16.83 - 27.61 349 27.61 - 38.40 182 38.40 - 49.18 98 49.18 - 59.97 51 59.97 - 70.75 13 70.75 - 81.54 6 81.54 - 92.32 4 92.32 - 103.11 1 103.11 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1668 r_work=0.1281 r_free=0.1676 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1676 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1277 r_free = 0.1663 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1277 r_free= 0.1663 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020042 | | target function (ls_wunit_k1) not normalized (work): 325.400910 | | target function (ls_wunit_k1) not normalized (free): 27.122907 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1277 0.1663 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1899 0.1897 0.2002 n_refl.: 17043 remove outliers: r(all,work,free)=0.1899 0.1897 0.2002 n_refl.: 17043 overall B=-0.37 to atoms: r(all,work,free)=0.1872 0.1869 0.1986 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1274 0.1660 n_refl.: 17043 remove outliers: r(all,work,free)=0.1292 0.1274 0.1660 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3461 303.824 277.598 0.611 1.003 0.360 11.894-9.307 99.02 97 4 0.1692 488.653 479.477 0.922 1.003 0.358 9.237-7.194 100.00 213 7 0.1852 399.669 395.867 0.961 1.003 0.351 7.162-5.571 100.00 427 22 0.1837 299.952 294.862 0.937 1.003 0.301 5.546-4.326 100.00 867 58 0.1038 411.786 409.688 0.962 1.003 0.210 4.315-3.360 100.00 1859 96 0.0927 391.612 390.828 1.017 1.002 0.191 3.356-2.611 100.00 3867 181 0.1299 257.267 255.863 1.011 1.001 0.091 2.608-2.000 99.99 8818 434 0.1350 167.694 166.394 1.014 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3369 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1660 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1660 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1660 | n_water=258 | time (s): 0.840 (total time: 0.840) Filter (dist) r_work=0.1277 r_free=0.1647 | n_water=255 | time (s): 21.640 (total time: 22.480) Filter (q & B) r_work=0.1277 r_free=0.1647 | n_water=253 | time (s): 1.470 (total time: 23.950) Compute maps r_work=0.1277 r_free=0.1647 | n_water=253 | time (s): 0.580 (total time: 24.530) Filter (map) r_work=0.1317 r_free=0.1639 | n_water=216 | time (s): 1.580 (total time: 26.110) Find peaks r_work=0.1317 r_free=0.1639 | n_water=216 | time (s): 0.610 (total time: 26.720) Add new water r_work=0.1526 r_free=0.1857 | n_water=374 | time (s): 2.170 (total time: 28.890) Refine new water occ: r_work=0.1329 r_free=0.1585 adp: r_work=0.1270 r_free=0.1583 occ: r_work=0.1275 r_free=0.1555 adp: r_work=0.1241 r_free=0.1564 occ: r_work=0.1242 r_free=0.1553 adp: r_work=0.1230 r_free=0.1554 ADP+occupancy (water only), MIN, final r_work=0.1230 r_free=0.1554 r_work=0.1230 r_free=0.1554 | n_water=374 | time (s): 10.990 (total time: 39.880) Filter (q & B) r_work=0.1233 r_free=0.1565 | n_water=365 | time (s): 1.740 (total time: 41.620) Filter (dist only) r_work=0.1234 r_free=0.1566 | n_water=364 | time (s): 29.280 (total time: 70.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.208521 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.912274 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1607 0.0400 0.008 0.9 2.2 0.5 0.0 0 12.104 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 16.07 4.00 4.182 21.060 0.912 0.018 11.95 16.18 4.24 4.163 21.375 0.912 0.017 Individual atomic B min max mean iso aniso Overall: 6.81 107.90 21.49 4.18 1891 0 Protein: 6.81 107.90 17.80 4.18 1519 0 Water: 8.61 68.18 36.62 N/A 364 0 Other: 24.46 42.76 32.76 N/A 8 0 Chain A: 6.81 107.90 19.62 N/A 1743 0 Chain S: 19.10 63.87 43.46 N/A 148 0 Histogram: Values Number of atoms 6.81 - 16.92 1016 16.92 - 27.03 393 27.03 - 37.14 218 37.14 - 47.25 160 47.25 - 57.36 63 57.36 - 67.47 30 67.47 - 77.57 4 77.57 - 87.68 4 87.68 - 97.79 1 97.79 - 107.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1618 r_work=0.1197 r_free=0.1621 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1621 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1614 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1193 r_free= 0.1614 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016964 | | target function (ls_wunit_k1) not normalized (work): 275.406171 | | target function (ls_wunit_k1) not normalized (free): 24.538426 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1193 0.1614 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1764 0.1756 0.1971 n_refl.: 17042 remove outliers: r(all,work,free)=0.1764 0.1756 0.1971 n_refl.: 17042 overall B=-0.40 to atoms: r(all,work,free)=0.1739 0.1729 0.1955 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1188 0.1609 n_refl.: 17042 remove outliers: r(all,work,free)=0.1207 0.1187 0.1609 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3218 300.658 287.034 0.592 1.005 0.340 11.894-9.307 99.02 97 4 0.1502 488.653 485.988 0.914 1.006 0.339 9.237-7.194 100.00 213 7 0.1673 399.669 399.674 0.973 1.006 0.295 7.162-5.571 100.00 427 22 0.1554 299.952 296.467 0.937 1.005 0.271 5.546-4.326 100.00 867 58 0.0896 411.786 409.231 0.960 1.005 0.211 4.315-3.360 100.00 1859 96 0.0808 391.612 390.627 1.016 1.003 0.201 3.356-2.611 100.00 3867 181 0.1207 257.267 256.615 1.013 1.001 0.121 2.608-2.000 99.99 8818 434 0.1325 167.694 166.665 1.021 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4131 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1609 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1609 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1609 | n_water=364 | time (s): 0.870 (total time: 0.870) Filter (dist) r_work=0.1187 r_free=0.1607 | n_water=363 | time (s): 27.900 (total time: 28.770) Filter (q & B) r_work=0.1187 r_free=0.1607 | n_water=363 | time (s): 0.950 (total time: 29.720) Compute maps r_work=0.1187 r_free=0.1607 | n_water=363 | time (s): 0.760 (total time: 30.480) Filter (map) r_work=0.1255 r_free=0.1637 | n_water=264 | time (s): 2.190 (total time: 32.670) Find peaks r_work=0.1255 r_free=0.1637 | n_water=264 | time (s): 0.610 (total time: 33.280) Add new water r_work=0.1445 r_free=0.1812 | n_water=412 | time (s): 1.520 (total time: 34.800) Refine new water occ: r_work=0.1243 r_free=0.1578 adp: r_work=0.1236 r_free=0.1583 occ: r_work=0.1219 r_free=0.1555 adp: r_work=0.1207 r_free=0.1556 occ: r_work=0.1200 r_free=0.1543 adp: r_work=0.1190 r_free=0.1542 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1542 r_work=0.1190 r_free=0.1542 | n_water=412 | time (s): 27.250 (total time: 62.050) Filter (q & B) r_work=0.1192 r_free=0.1551 | n_water=407 | time (s): 1.800 (total time: 63.850) Filter (dist only) r_work=0.1192 r_free=0.1554 | n_water=405 | time (s): 34.110 (total time: 97.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.895413 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.172664 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1173 0.1565 0.0392 0.009 1.0 4.8 0.5 0.0 0 0.948 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.73 15.65 3.92 4.294 21.585 0.173 4.994 11.54 15.77 4.24 4.865 21.509 0.173 4.974 Individual atomic B min max mean iso aniso Overall: 6.49 104.98 20.99 4.68 1932 0 Protein: 6.49 104.98 17.08 4.68 1519 0 Water: 8.77 60.57 35.47 N/A 405 0 Other: 24.45 40.68 31.58 N/A 8 0 Chain A: 6.49 104.98 18.85 N/A 1737 0 Chain S: 15.08 60.57 40.10 N/A 195 0 Histogram: Values Number of atoms 6.49 - 16.34 1066 16.34 - 26.19 352 26.19 - 36.04 223 36.04 - 45.89 166 45.89 - 55.74 83 55.74 - 65.59 28 65.59 - 75.44 6 75.44 - 85.29 3 85.29 - 95.14 3 95.14 - 104.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1154 r_free=0.1577 r_work=0.1153 r_free=0.1578 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1578 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1574 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1144 r_free= 0.1574 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.968710 | | target function (ml) not normalized (work): 80662.038905 | | target function (ml) not normalized (free): 4192.544749 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1144 0.1574 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1683 0.1676 0.1873 n_refl.: 17041 remove outliers: r(all,work,free)=0.1683 0.1676 0.1873 n_refl.: 17041 overall B=-0.39 to atoms: r(all,work,free)=0.1656 0.1648 0.1860 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1163 0.1142 0.1575 n_refl.: 17041 remove outliers: r(all,work,free)=0.1163 0.1142 0.1575 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3456 300.658 280.166 0.565 1.005 0.330 11.894-9.307 99.02 97 4 0.1739 488.653 480.403 0.905 1.006 0.314 9.237-7.194 100.00 213 7 0.1792 399.669 400.076 0.983 1.006 0.255 7.162-5.571 100.00 427 22 0.1611 299.952 294.738 0.940 1.006 0.241 5.546-4.326 100.00 867 58 0.0963 411.786 407.820 0.964 1.005 0.206 4.315-3.360 100.00 1859 96 0.0891 391.612 389.468 1.012 1.004 0.201 3.356-2.611 100.00 3867 181 0.1272 257.267 255.189 1.014 1.001 0.152 2.608-2.000 99.99 8818 434 0.1084 167.694 166.340 1.020 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4012 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1575 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1144 r_free=0.1573 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1573 | n_water=405 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1144 r_free=0.1573 | n_water=405 | time (s): 29.000 (total time: 29.900) Filter (q & B) r_work=0.1145 r_free=0.1575 | n_water=403 | time (s): 2.120 (total time: 32.020) Compute maps r_work=0.1145 r_free=0.1575 | n_water=403 | time (s): 0.790 (total time: 32.810) Filter (map) r_work=0.1199 r_free=0.1587 | n_water=311 | time (s): 2.180 (total time: 34.990) Find peaks r_work=0.1199 r_free=0.1587 | n_water=311 | time (s): 0.480 (total time: 35.470) Add new water r_work=0.1342 r_free=0.1714 | n_water=452 | time (s): 1.560 (total time: 37.030) Refine new water occ: r_work=0.1170 r_free=0.1534 adp: r_work=0.1164 r_free=0.1545 occ: r_work=0.1148 r_free=0.1510 adp: r_work=0.1141 r_free=0.1519 occ: r_work=0.1135 r_free=0.1495 adp: r_work=0.1128 r_free=0.1502 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1502 r_work=0.1128 r_free=0.1502 | n_water=452 | time (s): 36.770 (total time: 73.800) Filter (q & B) r_work=0.1131 r_free=0.1515 | n_water=439 | time (s): 1.800 (total time: 75.600) Filter (dist only) r_work=0.1136 r_free=0.1520 | n_water=438 | time (s): 34.400 (total time: 110.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.874699 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.174985 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1124 0.1551 0.0428 0.009 1.0 4.5 0.5 0.0 0 0.937 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 15.51 4.28 4.497 21.125 0.175 4.962 11.10 15.53 4.44 4.613 21.156 0.175 4.954 Individual atomic B min max mean iso aniso Overall: 5.98 103.29 21.02 4.87 1965 0 Protein: 5.98 103.29 16.69 4.86 1519 0 Water: 8.53 67.72 35.88 N/A 438 0 Other: 23.02 39.79 30.27 N/A 8 0 Chain A: 5.98 103.29 18.36 N/A 1735 0 Chain S: 15.62 67.72 41.10 N/A 230 0 Histogram: Values Number of atoms 5.98 - 15.71 1047 15.71 - 25.44 367 25.44 - 35.17 212 35.17 - 44.90 197 44.90 - 54.63 95 54.63 - 64.37 32 64.37 - 74.10 6 74.10 - 83.83 3 83.83 - 93.56 4 93.56 - 103.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1110 r_free=0.1553 r_work=0.1110 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1110 r_free = 0.1554 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1560 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1104 r_free= 0.1560 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.951260 | | target function (ml) not normalized (work): 80378.751558 | | target function (ml) not normalized (free): 4182.564087 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1104 0.1560 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1593 0.1580 0.1879 n_refl.: 17041 remove outliers: r(all,work,free)=0.1593 0.1580 0.1879 n_refl.: 17041 overall B=-0.31 to atoms: r(all,work,free)=0.1573 0.1559 0.1869 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1102 0.1552 n_refl.: 17041 remove outliers: r(all,work,free)=0.1122 0.1100 0.1552 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3562 302.843 275.206 0.549 1.002 0.328 11.894-9.307 99.02 97 4 0.1790 488.653 483.195 0.912 1.003 0.320 9.237-7.194 100.00 213 7 0.1746 399.669 399.966 0.986 1.004 0.225 7.162-5.571 100.00 427 22 0.1526 299.952 294.468 0.943 1.004 0.220 5.546-4.326 100.00 867 58 0.0931 411.786 408.427 0.964 1.003 0.192 4.315-3.360 100.00 1859 96 0.0851 391.612 389.373 1.009 1.003 0.180 3.356-2.611 100.00 3867 181 0.1226 257.267 255.357 1.008 1.001 0.141 2.608-2.000 99.99 8818 434 0.1039 167.694 166.590 1.006 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0846 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1552 After: r_work=0.1102 r_free=0.1551 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1551 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1551 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1551 | n_water=438 | time (s): 0.830 (total time: 0.830) Filter (dist) r_work=0.1102 r_free=0.1551 | n_water=438 | time (s): 34.980 (total time: 35.810) Filter (q & B) r_work=0.1102 r_free=0.1551 | n_water=437 | time (s): 1.790 (total time: 37.600) Compute maps r_work=0.1102 r_free=0.1551 | n_water=437 | time (s): 0.650 (total time: 38.250) Filter (map) r_work=0.1161 r_free=0.1542 | n_water=354 | time (s): 2.290 (total time: 40.540) Find peaks r_work=0.1161 r_free=0.1542 | n_water=354 | time (s): 0.520 (total time: 41.060) Add new water r_work=0.1271 r_free=0.1628 | n_water=483 | time (s): 1.780 (total time: 42.840) Refine new water occ: r_work=0.1133 r_free=0.1485 adp: r_work=0.1125 r_free=0.1487 occ: r_work=0.1114 r_free=0.1478 adp: r_work=0.1105 r_free=0.1478 occ: r_work=0.1100 r_free=0.1474 adp: r_work=0.1093 r_free=0.1475 ADP+occupancy (water only), MIN, final r_work=0.1093 r_free=0.1475 r_work=0.1093 r_free=0.1475 | n_water=483 | time (s): 25.070 (total time: 67.910) Filter (q & B) r_work=0.1095 r_free=0.1485 | n_water=471 | time (s): 2.090 (total time: 70.000) Filter (dist only) r_work=0.1095 r_free=0.1485 | n_water=471 | time (s): 37.580 (total time: 107.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.004324 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164061 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1107 0.1495 0.0388 0.010 1.0 3.8 0.5 0.0 0 1.002 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.07 14.95 3.88 4.574 21.022 0.164 4.941 10.97 14.78 3.81 4.692 21.074 0.164 4.933 Individual atomic B min max mean iso aniso Overall: 5.51 102.02 21.16 5.03 1998 0 Protein: 5.51 102.02 16.35 5.03 1519 0 Water: 8.03 62.33 36.54 N/A 471 0 Other: 22.35 38.25 28.79 N/A 8 0 Chain A: 5.51 102.02 18.01 N/A 1735 0 Chain S: 18.71 62.33 41.97 N/A 263 0 Histogram: Values Number of atoms 5.51 - 15.16 1033 15.16 - 24.81 380 24.81 - 34.46 203 34.46 - 44.11 193 44.11 - 53.76 129 53.76 - 63.41 41 63.41 - 73.06 9 73.06 - 82.71 4 82.71 - 92.37 3 92.37 - 102.02 3 =========================== Idealize ADP of riding H ========================== r_work=0.1097 r_free=0.1478 r_work=0.1097 r_free=0.1476 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1097 r_free = 0.1476 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1091 r_free = 0.1473 target_work(ml) = 4.927 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1091 r_free= 0.1473 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.926900 | | target function (ml) not normalized (work): 79978.374553 | | target function (ml) not normalized (free): 4157.459378 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1086 0.1397 5.4414 5.6873| | 2: 3.63 - 2.88 1.00 2711 122 0.1081 0.1363 5.209 5.302| | 3: 2.88 - 2.52 1.00 2681 148 0.1340 0.1654 5.1167 5.1913| | 4: 2.52 - 2.29 1.00 2661 139 0.0928 0.1466 4.6205 4.9239| | 5: 2.29 - 2.13 1.00 2678 122 0.0953 0.1479 4.5741 4.8881| | 6: 2.13 - 2.00 1.00 2692 117 0.1119 0.1674 4.5706 4.7628| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 8.84 1.00 0.96 6184.14| | 2: 3.63 - 2.88 2711 122 0.93 12.58 1.01 0.96 6184.14| | 3: 2.88 - 2.52 2681 148 0.88 18.64 0.99 0.96 6184.14| | 4: 2.52 - 2.29 2661 139 0.93 11.99 1.01 0.98 2098.43| | 5: 2.29 - 2.13 2678 122 0.91 14.10 1.00 0.98 2098.43| | 6: 2.13 - 2.00 2692 117 0.90 16.68 0.99 0.98 2098.43| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2098.43 max = 6184.14 mean = 4162.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.99 mean = 13.77| |phase err.(test): min = 0.00 max = 86.73 mean = 13.26| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1110 0.1091 0.1473 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1552 0.1539 0.1818 n_refl.: 17040 remove outliers: r(all,work,free)=0.1552 0.1539 0.1818 n_refl.: 17040 overall B=-0.25 to atoms: r(all,work,free)=0.1537 0.1524 0.1807 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1112 0.1093 0.1474 n_refl.: 17040 remove outliers: r(all,work,free)=0.1112 0.1093 0.1474 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3526 302.843 285.444 0.553 1.003 0.308 11.894-9.307 99.02 97 4 0.1845 488.653 482.107 0.909 1.005 0.294 9.237-7.194 100.00 213 7 0.1669 399.669 400.615 0.990 1.005 0.231 7.162-5.571 100.00 427 22 0.1474 299.952 295.345 0.940 1.005 0.207 5.546-4.326 100.00 867 58 0.0908 411.786 408.917 0.962 1.004 0.191 4.315-3.360 100.00 1859 96 0.0856 391.612 389.405 1.004 1.003 0.181 3.356-2.611 100.00 3867 181 0.1231 257.267 255.155 1.002 1.000 0.111 2.608-2.000 99.99 8818 434 0.1028 167.694 166.395 0.997 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8646 ================= 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 : 0.2785 0.1771 0.082 5.364 8.8 119.3 19.9 258 0.000 1_bss: 0.1610 0.1663 0.082 5.364 8.4 118.9 19.5 258 0.000 1_settarget: 0.1610 0.1663 0.082 5.364 8.4 118.9 19.5 258 0.000 1_nqh: 0.1613 0.1663 0.082 5.364 8.4 118.9 19.5 258 0.003 1_weight: 0.1613 0.1663 0.082 5.364 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1352 0.1640 0.009 0.972 8.4 118.9 19.5 258 0.153 1_adp: 0.1278 0.1668 0.009 0.972 6.0 113.9 19.9 258 0.153 1_regHadp: 0.1281 0.1676 0.009 0.972 6.0 113.9 19.9 258 0.153 1_occ: 0.1277 0.1663 0.009 0.972 6.0 113.9 19.9 258 0.153 2_bss: 0.1274 0.1660 0.009 0.972 5.7 113.5 19.5 258 0.153 2_settarget: 0.1274 0.1660 0.009 0.972 5.7 113.5 19.5 258 0.153 2_updatecdl: 0.1274 0.1660 0.009 0.995 5.7 113.5 19.5 258 0.153 2_nqh: 0.1274 0.1660 0.009 0.995 5.7 113.5 19.5 258 0.153 2_sol: 0.1234 0.1566 0.009 0.995 5.7 112.9 20.9 364 n/a 2_weight: 0.1234 0.1566 0.009 0.995 5.7 112.9 20.9 364 n/a 2_xyzrec: 0.1207 0.1607 0.008 0.928 5.7 112.9 20.9 364 n/a 2_adp: 0.1195 0.1618 0.008 0.928 6.8 107.9 21.5 364 n/a 2_regHadp: 0.1197 0.1621 0.008 0.928 6.8 107.9 21.5 364 n/a 2_occ: 0.1193 0.1614 0.008 0.928 6.8 107.9 21.5 364 n/a 3_bss: 0.1187 0.1609 0.008 0.928 6.4 107.5 21.1 364 n/a 3_settarget: 0.1187 0.1609 0.008 0.928 6.4 107.5 21.1 364 n/a 3_updatecdl: 0.1187 0.1609 0.008 0.934 6.4 107.5 21.1 364 n/a 3_nqh: 0.1187 0.1609 0.008 0.934 6.4 107.5 21.1 364 n/a 3_sol: 0.1192 0.1554 0.008 0.934 6.4 107.5 21.1 405 n/a 3_weight: 0.1192 0.1554 0.008 0.934 6.4 107.5 21.1 405 n/a 3_xyzrec: 0.1173 0.1565 0.009 0.964 6.4 107.5 21.1 405 n/a 3_adp: 0.1154 0.1577 0.009 0.964 6.5 105.0 21.0 405 n/a 3_regHadp: 0.1153 0.1578 0.009 0.964 6.5 105.0 21.0 405 n/a 3_occ: 0.1144 0.1574 0.009 0.964 6.5 105.0 21.0 405 n/a 4_bss: 0.1142 0.1575 0.009 0.964 6.1 104.6 20.6 405 n/a 4_settarget: 0.1142 0.1575 0.009 0.964 6.1 104.6 20.6 405 n/a 4_updatecdl: 0.1142 0.1575 0.009 0.963 6.1 104.6 20.6 405 n/a 4_nqh: 0.1144 0.1573 0.009 0.963 6.1 104.6 20.6 405 n/a 4_sol: 0.1136 0.1520 0.009 0.963 6.1 104.6 21.0 438 n/a 4_weight: 0.1136 0.1520 0.009 0.963 6.1 104.6 21.0 438 n/a 4_xyzrec: 0.1124 0.1551 0.009 0.968 6.1 104.6 21.0 438 n/a 4_adp: 0.1110 0.1553 0.009 0.968 6.0 103.3 21.0 438 n/a 4_regHadp: 0.1110 0.1554 0.009 0.968 6.0 103.3 21.0 438 n/a 4_occ: 0.1104 0.1560 0.009 0.968 6.0 103.3 21.0 438 n/a 5_bss: 0.1100 0.1552 0.009 0.968 5.7 103.0 20.7 438 n/a 5_settarget: 0.1100 0.1552 0.009 0.968 5.7 103.0 20.7 438 n/a 5_updatecdl: 0.1100 0.1552 0.009 0.970 5.7 103.0 20.7 438 n/a 5_setrh: 0.1102 0.1551 0.009 0.970 5.7 103.0 20.7 438 n/a 5_nqh: 0.1102 0.1551 0.009 0.970 5.7 103.0 20.7 438 n/a 5_sol: 0.1095 0.1485 0.009 0.970 5.7 103.0 21.1 471 n/a 5_weight: 0.1095 0.1485 0.009 0.970 5.7 103.0 21.1 471 n/a 5_xyzrec: 0.1107 0.1495 0.010 1.016 5.7 103.0 21.1 471 n/a 5_adp: 0.1097 0.1478 0.010 1.016 5.5 102.0 21.2 471 n/a 5_regHadp: 0.1097 0.1476 0.010 1.016 5.5 102.0 21.2 471 n/a 5_occ: 0.1091 0.1473 0.010 1.016 5.5 102.0 21.2 471 n/a end: 0.1093 0.1474 0.010 1.016 5.3 101.8 20.9 471 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7766834_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7766834_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2100 Refinement macro-cycles (run) : 915.8000 Write final files (write_after_run_outputs) : 20.2300 Total : 939.2400 Total CPU time: 16.05 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:04 PST -0800 (1735494064.49 s) Start R-work = 0.1610, R-free = 0.1663 Final R-work = 0.1093, R-free = 0.1474 =============================================================================== Job complete usr+sys time: 985.21 seconds wall clock time: 16 minutes 48.12 seconds (1008.12 seconds total)