Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2353655.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" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2353655.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2353655.pdb" } 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 =============================================================================== 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: 1.97, per 1000 atoms: 0.58 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: 0.43 Conformation dependent library (CDL) restraints added in 127.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 532 0.91 - 1.16: 1109 1.16 - 1.42: 624 1.42 - 1.67: 838 1.67 - 1.92: 50 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 0.974 0.262 1.19e-02 7.06e+03 4.84e+02 bond pdb=" CA ILE A 21 " pdb=" C ILE A 21 " ideal model delta sigma weight residual 1.523 1.699 -0.176 9.20e-03 1.18e+04 3.64e+02 bond pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 1.237 1.011 0.226 1.19e-02 7.06e+03 3.59e+02 bond pdb=" ND1 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 1.321 1.132 0.189 1.00e-02 1.00e+04 3.57e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.639 -0.100 5.40e-03 3.43e+04 3.41e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 3034 4.38 - 8.76: 1829 8.76 - 13.13: 729 13.13 - 17.51: 159 17.51 - 21.89: 26 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 134.62 -13.12 1.00e+00 1.00e+00 1.72e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.15 137.09 -14.94 1.14e+00 7.69e-01 1.72e+02 angle pdb=" CA PHE A 119 " pdb=" CB PHE A 119 " pdb=" CG PHE A 119 " ideal model delta sigma weight residual 113.80 126.88 -13.08 1.00e+00 1.00e+00 1.71e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.19 109.67 11.52 9.40e-01 1.13e+00 1.50e+02 angle pdb=" O PRO A 158 " pdb=" C PRO A 158 " pdb=" N GLY A 159 " ideal model delta sigma weight residual 122.23 136.92 -14.69 1.20e+00 6.94e-01 1.50e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1289 16.75 - 33.50: 132 33.50 - 50.25: 43 50.25 - 67.00: 15 67.00 - 83.75: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CA ALA A 183 " pdb=" CB ALA A 183 " ideal model delta harmonic sigma weight residual 122.90 143.06 -20.16 0 2.50e+00 1.60e-01 6.50e+01 dihedral pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CA BLEU A 153 " pdb=" CB BLEU A 153 " ideal model delta harmonic sigma weight residual 122.80 104.46 18.34 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" N PRO A 22 " pdb=" C PRO A 22 " pdb=" CA PRO A 22 " pdb=" CB PRO A 22 " ideal model delta harmonic sigma weight residual 115.10 132.73 -17.63 0 2.50e+00 1.60e-01 4.98e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.225: 105 0.225 - 0.449: 85 0.449 - 0.673: 38 0.673 - 0.897: 8 0.897 - 1.122: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.61 -1.12 2.00e-01 2.50e+01 3.15e+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 -1.56 -1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 1.58 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.090 9.50e-02 1.11e+02 7.28e-02 1.00e+02 pdb=" NE ARG A 156 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " 0.069 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " -0.077 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " -0.034 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " -0.066 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.003 2.00e-02 2.50e+03 5.67e-02 9.65e+01 pdb=" CG BTYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.070 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.048 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.114 2.00e-02 2.50e+03 6.49e-02 9.46e+01 pdb=" CG HIS A 138 " -0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.068 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 984 2.31 - 2.88: 8064 2.88 - 3.46: 10527 3.46 - 4.03: 15145 4.03 - 4.60: 21916 Nonbonded interactions: 56636 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.738 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.766 2.100 nonbonded pdb=" HE3ALYS A 132 " pdb=" HO2ADTT A 201 " model vdw 1.792 2.270 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.808 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.832 2.450 ... (remaining 56631 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_2353655_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= 0.1817 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.401400 | | target function (ml) not normalized (work): 71491.946787 | | target function (ml) not normalized (free): 3267.082356 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3190 0.2152 7.5362 5.0415| | 2: 3.63 - 2.88 1.00 2711 122 0.2634 0.1679 4.3269 4.3177| | 3: 2.88 - 2.52 1.00 2682 148 0.2558 0.1702 4.1818 4.1958| | 4: 2.52 - 2.29 1.00 2661 139 0.2548 0.1584 3.5123 3.5983| | 5: 2.29 - 2.13 1.00 2678 122 0.2679 0.1497 3.3881 3.4303| | 6: 2.13 - 2.00 1.00 2692 117 0.2725 0.1807 3.2995 3.411| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.46 0.77 0.23 1308.93| | 2: 3.63 - 2.88 2711 122 0.83 23.80 1.31 0.23 1308.93| | 3: 2.88 - 2.52 2682 148 0.73 32.96 1.29 0.23 1308.93| | 4: 2.52 - 2.29 2661 139 0.94 11.09 1.30 0.26 131.93| | 5: 2.29 - 2.13 2678 122 0.92 13.46 1.32 0.26 131.93| | 6: 2.13 - 2.00 2692 117 0.90 16.11 1.33 0.26 131.93| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 131.93 max = 1308.93 mean = 726.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.79 mean = 19.15| |phase err.(test): min = 0.00 max = 89.70 mean = 19.11| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.262 1557 Z= 5.579 Angle : 5.302 19.172 2118 Z= 3.691 Chirality : 0.374 1.122 243 Planarity : 0.033 0.109 284 Dihedral : 13.894 83.747 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 26.49 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.51), residues: 224 helix: -2.43 (0.37), residues: 108 sheet: 0.13 (0.94), residues: 28 loop : 0.11 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.027 ARG A 145 TYR 0.086 0.035 TYR A 141 PHE 0.103 0.033 PHE A 119 HIS 0.053 0.028 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2785 r_free= 0.1817 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.401400 | | target function (ml) not normalized (work): 71491.946787 | | target function (ml) not normalized (free): 3267.082356 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2967 percent. r_work = 0.2915 r_free = 0.2001 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2862 0.2915 0.2001 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2862 0.2915 0.2001 n_refl.: 17050 remove outliers: r(all,work,free)=0.2153 0.2164 0.2001 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2126 0.2136 0.1985 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1615 0.1612 0.1672 n_refl.: 17045 remove outliers: r(all,work,free)=0.1614 0.1612 0.1672 n_refl.: 17044 ======================== 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 32.574-12.150 100.00 89 5 0.4104 394.673 360.819 0.648 1.019 0.399 11.894-9.307 99.02 97 4 0.1895 633.462 613.219 0.925 1.020 0.390 9.237-7.194 100.00 213 7 0.2202 518.108 510.699 0.957 1.019 0.345 7.162-5.571 100.00 427 22 0.2302 388.841 375.791 0.915 1.017 0.278 5.546-4.326 100.00 867 58 0.1415 533.816 528.294 0.954 1.014 0.224 4.315-3.360 100.00 1859 96 0.1305 507.664 503.304 1.015 1.008 0.217 3.356-2.611 100.00 3867 181 0.1644 333.506 329.432 1.013 0.998 0.044 2.608-2.000 99.99 8818 434 0.1638 217.389 213.551 1.038 0.982 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4566 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1612 r_free=0.1672 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1613 r_free=0.1679 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.345498 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.813304 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 0.1351 0.1643 0.0292 0.009 1.0 1.0 0.5 0.0 0 11.673 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.43 2.92 3.013 18.451 0.813 0.023 12.79 16.60 3.81 3.564 18.719 0.813 0.021 Individual atomic B min max mean iso aniso Overall: 6.60 113.89 19.99 4.02 1785 0 Protein: 6.60 112.63 17.24 4.02 1519 0 Water: 8.70 113.89 35.96 N/A 258 0 Other: 22.00 36.31 26.32 N/A 8 0 Chain A: 6.60 113.89 19.99 N/A 1785 0 Histogram: Values Number of atoms 6.60 - 17.33 1107 17.33 - 28.06 326 28.06 - 38.79 180 38.79 - 49.52 99 49.52 - 60.25 47 60.25 - 70.98 12 70.98 - 81.70 6 81.70 - 92.43 4 92.43 - 103.16 1 103.16 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1660 r_work=0.1282 r_free=0.1666 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1666 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 = 0.1276 r_free = 0.1656 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1276 r_free= 0.1656 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020063 | | target function (ls_wunit_k1) not normalized (work): 325.767878 | | target function (ls_wunit_k1) not normalized (free): 27.189758 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1276 0.1656 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1914 0.1914 0.1984 n_refl.: 17044 remove outliers: r(all,work,free)=0.1914 0.1914 0.1984 n_refl.: 17044 overall B=-0.40 to atoms: r(all,work,free)=0.1885 0.1884 0.1967 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1646 n_refl.: 17044 remove outliers: r(all,work,free)=0.1293 0.1275 0.1646 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 0.3545 303.043 279.162 0.625 1.010 0.368 11.894-9.307 99.02 97 4 0.1690 487.396 477.520 0.919 1.011 0.367 9.237-7.194 100.00 213 7 0.1817 398.641 395.864 0.960 1.010 0.351 7.162-5.571 100.00 427 22 0.1832 299.181 294.181 0.929 1.009 0.264 5.546-4.326 100.00 867 58 0.1046 410.727 408.479 0.958 1.008 0.215 4.315-3.360 100.00 1859 96 0.0929 390.605 390.321 1.018 1.005 0.201 3.356-2.611 100.00 3867 181 0.1299 256.605 255.334 1.016 1.000 0.091 2.608-2.000 99.99 8818 434 0.1351 167.263 165.759 1.025 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4266 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1646 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1277 r_free=0.1650 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1650 | n_water=258 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1286 r_free=0.1639 | n_water=253 | time (s): 20.260 (total time: 21.030) Filter (q & B) r_work=0.1287 r_free=0.1639 | n_water=251 | time (s): 2.040 (total time: 23.070) Compute maps r_work=0.1287 r_free=0.1639 | n_water=251 | time (s): 0.800 (total time: 23.870) Filter (map) r_work=0.1320 r_free=0.1639 | n_water=213 | time (s): 1.930 (total time: 25.800) Find peaks r_work=0.1320 r_free=0.1639 | n_water=213 | time (s): 0.660 (total time: 26.460) Add new water r_work=0.1528 r_free=0.1881 | n_water=365 | time (s): 2.180 (total time: 28.640) Refine new water occ: r_work=0.1326 r_free=0.1598 adp: r_work=0.1275 r_free=0.1597 occ: r_work=0.1281 r_free=0.1573 adp: r_work=0.1250 r_free=0.1575 occ: r_work=0.1252 r_free=0.1566 adp: r_work=0.1241 r_free=0.1563 ADP+occupancy (water only), MIN, final r_work=0.1241 r_free=0.1563 r_work=0.1241 r_free=0.1563 | n_water=365 | time (s): 26.090 (total time: 54.730) Filter (q & B) r_work=0.1245 r_free=0.1566 | n_water=353 | time (s): 1.800 (total time: 56.530) Filter (dist only) r_work=0.1245 r_free=0.1568 | n_water=352 | time (s): 28.000 (total time: 84.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.052716 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.011144 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 0.1223 0.1592 0.0369 0.008 0.9 2.2 0.5 0.0 0 12.026 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.23 15.92 3.69 4.141 20.974 1.011 0.019 12.03 16.18 4.14 4.234 21.276 1.011 0.018 Individual atomic B min max mean iso aniso Overall: 6.61 107.23 21.25 4.32 1879 0 Protein: 6.61 107.23 17.76 4.31 1519 0 Water: 8.79 65.77 35.93 N/A 352 0 Other: 25.90 48.18 37.26 N/A 8 0 Chain A: 6.61 107.23 19.56 N/A 1740 0 Chain S: 18.93 65.18 42.38 N/A 139 0 Histogram: Values Number of atoms 6.61 - 16.68 1021 16.68 - 26.74 378 26.74 - 36.80 217 36.80 - 46.86 162 46.86 - 56.92 59 56.92 - 66.99 31 66.99 - 77.05 3 77.05 - 87.11 4 87.11 - 97.17 2 97.17 - 107.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1618 r_work=0.1204 r_free=0.1618 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1618 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1616 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 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= 0.1204 r_free= 0.1616 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017338 | | target function (ls_wunit_k1) not normalized (work): 281.476081 | | target function (ls_wunit_k1) not normalized (free): 25.494047 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1204 0.1616 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1761 0.1754 0.1914 n_refl.: 17042 remove outliers: r(all,work,free)=0.1761 0.1754 0.1914 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1736 0.1730 0.1898 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1198 0.1611 n_refl.: 17042 remove outliers: r(all,work,free)=0.1218 0.1198 0.1611 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 0.3411 303.043 281.349 0.607 1.005 0.350 11.894-9.307 99.02 97 4 0.1568 487.396 482.043 0.916 1.006 0.350 9.237-7.194 100.00 213 7 0.1662 398.641 400.024 0.971 1.006 0.280 7.162-5.571 100.00 427 22 0.1614 299.181 295.532 0.931 1.005 0.261 5.546-4.326 100.00 867 58 0.0884 410.727 407.604 0.959 1.005 0.210 4.315-3.360 100.00 1859 96 0.0835 390.605 389.703 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1207 256.605 255.825 1.012 1.001 0.048 2.608-2.000 99.99 8818 434 0.1332 167.263 166.239 1.017 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3470 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1611 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1611 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1611 | n_water=352 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1199 r_free=0.1612 | n_water=350 | time (s): 27.770 (total time: 28.540) Filter (q & B) r_work=0.1199 r_free=0.1612 | n_water=350 | time (s): 0.890 (total time: 29.430) Compute maps r_work=0.1199 r_free=0.1612 | n_water=350 | time (s): 0.710 (total time: 30.140) Filter (map) r_work=0.1261 r_free=0.1631 | n_water=262 | time (s): 2.310 (total time: 32.450) Find peaks r_work=0.1261 r_free=0.1631 | n_water=262 | time (s): 0.590 (total time: 33.040) Add new water r_work=0.1443 r_free=0.1750 | n_water=416 | time (s): 2.080 (total time: 35.120) Refine new water occ: r_work=0.1248 r_free=0.1578 adp: r_work=0.1238 r_free=0.1577 occ: r_work=0.1224 r_free=0.1554 adp: r_work=0.1211 r_free=0.1555 occ: r_work=0.1206 r_free=0.1542 adp: r_work=0.1194 r_free=0.1540 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1540 r_work=0.1194 r_free=0.1540 | n_water=416 | time (s): 36.510 (total time: 71.630) Filter (q & B) r_work=0.1196 r_free=0.1541 | n_water=407 | time (s): 1.800 (total time: 73.430) Filter (dist only) r_work=0.1196 r_free=0.1541 | n_water=407 | time (s): 31.230 (total time: 104.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.859210 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.141664 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 0.1170 0.1540 0.0370 0.009 0.9 3.5 0.5 0.0 0 0.930 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.70 15.40 3.70 4.376 21.624 0.142 4.995 11.53 15.48 3.95 4.955 21.506 0.142 4.973 Individual atomic B min max mean iso aniso Overall: 6.12 103.83 20.93 4.66 1934 0 Protein: 6.12 103.83 17.01 4.65 1519 0 Water: 8.23 62.03 35.24 N/A 407 0 Other: 27.66 47.80 36.52 N/A 8 0 Chain A: 6.12 103.83 18.76 N/A 1735 0 Chain S: 15.35 62.03 39.84 N/A 199 0 Histogram: Values Number of atoms 6.12 - 15.89 1050 15.89 - 25.66 354 25.66 - 35.43 226 35.43 - 45.20 185 45.20 - 54.97 76 54.97 - 64.74 29 64.74 - 74.51 5 74.51 - 84.29 4 84.29 - 94.06 3 94.06 - 103.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1548 r_work=0.1153 r_free=0.1551 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1551 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1549 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1144 r_free= 0.1549 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.967854 | | target function (ml) not normalized (work): 80653.113487 | | target function (ml) not normalized (free): 4192.007628 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1164 0.1144 0.1549 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1671 0.1665 0.1842 n_refl.: 17042 remove outliers: r(all,work,free)=0.1671 0.1665 0.1842 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1646 0.1639 0.1828 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1141 0.1553 n_refl.: 17042 remove outliers: r(all,work,free)=0.1161 0.1141 0.1553 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 0.3582 299.556 278.355 0.571 1.006 0.337 11.894-9.307 99.02 97 4 0.1630 487.396 479.236 0.910 1.007 0.335 9.237-7.194 100.00 213 7 0.1740 398.641 399.989 0.985 1.007 0.259 7.162-5.571 100.00 427 22 0.1605 299.181 292.734 0.932 1.006 0.225 5.546-4.326 100.00 867 58 0.0933 410.727 406.954 0.963 1.006 0.210 4.315-3.360 100.00 1859 96 0.0893 390.605 388.530 1.011 1.004 0.201 3.356-2.611 100.00 3867 181 0.1267 256.605 254.220 1.012 1.001 0.142 2.608-2.000 99.99 8818 434 0.1094 167.263 165.928 1.017 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3279 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1141 r_free=0.1553 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1141 r_free=0.1553 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1141 r_free=0.1553 | n_water=407 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1141 r_free=0.1557 | n_water=406 | time (s): 32.400 (total time: 33.320) Filter (q & B) r_work=0.1141 r_free=0.1557 | n_water=405 | time (s): 1.770 (total time: 35.090) Compute maps r_work=0.1141 r_free=0.1557 | n_water=405 | time (s): 0.670 (total time: 35.760) Filter (map) r_work=0.1194 r_free=0.1547 | n_water=315 | time (s): 2.280 (total time: 38.040) Find peaks r_work=0.1194 r_free=0.1547 | n_water=315 | time (s): 0.570 (total time: 38.610) Add new water r_work=0.1325 r_free=0.1669 | n_water=447 | time (s): 1.750 (total time: 40.360) Refine new water occ: r_work=0.1169 r_free=0.1548 adp: r_work=0.1163 r_free=0.1544 occ: r_work=0.1148 r_free=0.1529 adp: r_work=0.1142 r_free=0.1524 occ: r_work=0.1134 r_free=0.1517 adp: r_work=0.1129 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1512 r_work=0.1129 r_free=0.1512 | n_water=447 | time (s): 39.600 (total time: 79.960) Filter (q & B) r_work=0.1133 r_free=0.1521 | n_water=436 | time (s): 1.380 (total time: 81.340) Filter (dist only) r_work=0.1133 r_free=0.1521 | n_water=436 | time (s): 30.810 (total time: 112.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.043087 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.166941 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 0.1120 0.1558 0.0438 0.010 1.0 4.2 0.5 0.0 0 1.022 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 15.58 4.38 4.480 21.049 0.167 4.959 11.08 15.64 4.56 4.697 21.042 0.167 4.954 Individual atomic B min max mean iso aniso Overall: 5.21 101.23 20.85 4.84 1963 0 Protein: 5.21 101.23 16.51 4.83 1519 0 Water: 8.11 63.93 35.70 N/A 436 0 Other: 26.95 48.23 36.26 N/A 8 0 Chain A: 5.21 101.23 18.21 N/A 1734 0 Chain S: 14.78 63.93 40.90 N/A 229 0 Histogram: Values Number of atoms 5.21 - 14.81 975 14.81 - 24.41 416 24.41 - 34.01 214 34.01 - 43.62 194 43.62 - 53.22 114 53.22 - 62.82 32 62.82 - 72.42 8 72.42 - 82.03 4 82.03 - 91.63 4 91.63 - 101.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1564 r_work=0.1108 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1563 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1559 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1559 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.948863 | | target function (ml) not normalized (work): 80339.848297 | | target function (ml) not normalized (free): 4188.111485 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1100 0.1559 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1601 0.1590 0.1834 n_refl.: 17041 remove outliers: r(all,work,free)=0.1601 0.1590 0.1834 n_refl.: 17041 overall B=-0.30 to atoms: r(all,work,free)=0.1582 0.1571 0.1824 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1099 0.1552 n_refl.: 17041 remove outliers: r(all,work,free)=0.1121 0.1099 0.1552 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 0.3605 299.556 275.412 0.563 1.001 0.340 11.894-9.307 99.02 97 4 0.1693 487.396 481.933 0.920 1.002 0.320 9.237-7.194 100.00 213 7 0.1661 398.641 401.379 0.991 1.002 0.250 7.162-5.571 100.00 427 22 0.1568 299.181 293.558 0.938 1.002 0.210 5.546-4.326 100.00 867 58 0.0912 410.727 407.501 0.966 1.002 0.201 4.315-3.360 100.00 1859 96 0.0853 390.605 388.184 1.008 1.002 0.201 3.356-2.611 100.00 3867 181 0.1212 256.605 254.340 1.006 1.001 0.131 2.608-2.000 99.99 8818 434 0.1053 167.263 166.036 1.000 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0228 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1099 r_free=0.1552 After: r_work=0.1101 r_free=0.1551 ================================== NQH flips ================================== r_work=0.1101 r_free=0.1551 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1101 r_free=0.1551 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1101 r_free=0.1551 | n_water=436 | time (s): 0.890 (total time: 0.890) Filter (dist) r_work=0.1101 r_free=0.1551 | n_water=436 | time (s): 32.390 (total time: 33.280) Filter (q & B) r_work=0.1101 r_free=0.1552 | n_water=434 | time (s): 1.500 (total time: 34.780) Compute maps r_work=0.1101 r_free=0.1552 | n_water=434 | time (s): 0.600 (total time: 35.380) Filter (map) r_work=0.1159 r_free=0.1579 | n_water=349 | time (s): 1.730 (total time: 37.110) Find peaks r_work=0.1159 r_free=0.1579 | n_water=349 | time (s): 0.430 (total time: 37.540) Add new water r_work=0.1300 r_free=0.1674 | n_water=488 | time (s): 1.410 (total time: 38.950) Refine new water occ: r_work=0.1141 r_free=0.1513 adp: r_work=0.1133 r_free=0.1517 occ: r_work=0.1116 r_free=0.1501 adp: r_work=0.1107 r_free=0.1504 occ: r_work=0.1098 r_free=0.1492 adp: r_work=0.1091 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1091 r_free=0.1496 r_work=0.1091 r_free=0.1496 | n_water=488 | time (s): 40.960 (total time: 79.910) Filter (q & B) r_work=0.1095 r_free=0.1503 | n_water=478 | time (s): 1.570 (total time: 81.480) Filter (dist only) r_work=0.1095 r_free=0.1503 | n_water=478 | time (s): 36.510 (total time: 117.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.929076 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.155834 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 0.1119 0.1514 0.0395 0.010 1.0 5.4 0.5 0.0 0 0.965 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.14 3.95 4.535 20.919 0.156 4.947 11.06 15.04 3.98 4.587 20.992 0.156 4.937 Individual atomic B min max mean iso aniso Overall: 5.16 100.60 21.19 4.98 2005 0 Protein: 5.16 100.60 16.25 4.96 1519 0 Water: 8.01 64.49 36.65 N/A 478 0 Other: 27.14 47.96 35.39 N/A 8 0 Chain A: 5.16 100.60 17.91 N/A 1734 0 Chain S: 18.58 64.49 42.20 N/A 271 0 Histogram: Values Number of atoms 5.16 - 14.70 994 14.70 - 24.25 399 24.25 - 33.79 212 33.79 - 43.34 198 43.34 - 52.88 143 52.88 - 62.42 38 62.42 - 71.97 11 71.97 - 81.51 3 81.51 - 91.05 3 91.05 - 100.60 4 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1504 r_work=0.1106 r_free=0.1503 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1503 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1097 r_free = 0.1505 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1097 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.931583 | | target function (ml) not normalized (work): 80059.312383 | | target function (ml) not normalized (free): 4164.208259 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1104 0.1387 5.4439 5.6186| | 2: 3.63 - 2.88 1.00 2711 122 0.1063 0.1491 5.2043 5.3704| | 3: 2.88 - 2.52 1.00 2681 148 0.1341 0.1667 5.1168 5.1958| | 4: 2.52 - 2.29 1.00 2661 139 0.0945 0.1566 4.6349 4.9851| | 5: 2.29 - 2.13 1.00 2678 122 0.0970 0.1458 4.5852 4.8911| | 6: 2.13 - 2.00 1.00 2692 117 0.1122 0.1658 4.5753 4.761| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2811 159 0.95 8.82 1.00 0.95 6251.11| | 2: 3.63 - 2.88 2711 122 0.92 12.74 1.01 0.95 6251.11| | 3: 2.88 - 2.52 2681 148 0.88 18.90 0.99 0.95 6251.11| | 4: 2.52 - 2.29 2661 139 0.93 12.17 1.01 0.97 2138.00| | 5: 2.29 - 2.13 2678 122 0.91 14.20 1.00 0.97 2138.00| | 6: 2.13 - 2.00 2692 117 0.89 16.95 0.99 0.97 2138.00| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2138.00 max = 6251.11 mean = 4216.34| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.96 mean = 13.93| |phase err.(test): min = 0.00 max = 88.86 mean = 13.54| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1116 0.1097 0.1505 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1568 0.1558 0.1783 n_refl.: 17041 remove outliers: r(all,work,free)=0.1568 0.1558 0.1783 n_refl.: 17041 overall B=-0.24 to atoms: r(all,work,free)=0.1553 0.1543 0.1775 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1117 0.1097 0.1503 n_refl.: 17041 remove outliers: r(all,work,free)=0.1117 0.1097 0.1503 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 0.3541 299.556 278.665 0.555 1.002 0.340 11.894-9.307 99.02 97 4 0.1773 487.396 481.296 0.919 1.003 0.320 9.237-7.194 100.00 213 7 0.1683 398.641 401.883 0.989 1.003 0.230 7.162-5.571 100.00 427 22 0.1509 299.181 294.847 0.935 1.003 0.190 5.546-4.326 100.00 867 58 0.0919 410.727 407.787 0.966 1.003 0.190 4.315-3.360 100.00 1859 96 0.0864 390.605 388.334 1.004 1.002 0.191 3.356-2.611 100.00 3867 181 0.1211 256.605 254.099 1.002 1.001 0.058 2.608-2.000 99.99 8818 434 0.1044 167.263 165.986 0.992 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8351 ================= 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 0.1817 0.083 5.302 8.8 119.3 19.9 258 0.000 1_bss: 0.1612 0.1672 0.083 5.302 8.4 118.9 19.5 258 0.000 1_settarget: 0.1612 0.1672 0.083 5.302 8.4 118.9 19.5 258 0.000 1_nqh: 0.1613 0.1679 0.083 5.302 8.4 118.9 19.5 258 0.006 1_weight: 0.1613 0.1679 0.083 5.302 8.4 118.9 19.5 258 0.006 1_xyzrec: 0.1351 0.1643 0.009 0.984 8.4 118.9 19.5 258 0.149 1_adp: 0.1279 0.1660 0.009 0.984 6.6 113.9 20.0 258 0.149 1_regHadp: 0.1282 0.1666 0.009 0.984 6.6 113.9 20.0 258 0.149 1_occ: 0.1276 0.1656 0.009 0.984 6.6 113.9 20.0 258 0.149 2_bss: 0.1275 0.1646 0.009 0.984 6.2 113.5 19.6 258 0.149 2_settarget: 0.1275 0.1646 0.009 0.984 6.2 113.5 19.6 258 0.149 2_updatecdl: 0.1275 0.1646 0.009 0.994 6.2 113.5 19.6 258 0.149 2_nqh: 0.1277 0.1650 0.009 0.994 6.2 113.5 19.6 258 0.146 2_sol: 0.1245 0.1568 0.009 0.994 6.2 112.2 20.7 352 n/a 2_weight: 0.1245 0.1568 0.009 0.994 6.2 112.2 20.7 352 n/a 2_xyzrec: 0.1223 0.1592 0.008 0.925 6.2 112.2 20.7 352 n/a 2_adp: 0.1203 0.1618 0.008 0.925 6.6 107.2 21.2 352 n/a 2_regHadp: 0.1204 0.1618 0.008 0.925 6.6 107.2 21.2 352 n/a 2_occ: 0.1204 0.1616 0.008 0.925 6.6 107.2 21.2 352 n/a 3_bss: 0.1198 0.1611 0.008 0.925 6.2 106.9 20.9 352 n/a 3_settarget: 0.1198 0.1611 0.008 0.925 6.2 106.9 20.9 352 n/a 3_updatecdl: 0.1198 0.1611 0.008 0.925 6.2 106.9 20.9 352 n/a 3_nqh: 0.1198 0.1611 0.008 0.925 6.2 106.9 20.9 352 n/a 3_sol: 0.1196 0.1541 0.008 0.925 6.2 106.9 21.1 407 n/a 3_weight: 0.1196 0.1541 0.008 0.925 6.2 106.9 21.1 407 n/a 3_xyzrec: 0.1170 0.1540 0.009 0.949 6.2 106.9 21.1 407 n/a 3_adp: 0.1153 0.1548 0.009 0.949 6.1 103.8 20.9 407 n/a 3_regHadp: 0.1153 0.1551 0.009 0.949 6.1 103.8 20.9 407 n/a 3_occ: 0.1144 0.1549 0.009 0.949 6.1 103.8 20.9 407 n/a 4_bss: 0.1141 0.1553 0.009 0.949 5.7 103.5 20.6 407 n/a 4_settarget: 0.1141 0.1553 0.009 0.949 5.7 103.5 20.6 407 n/a 4_updatecdl: 0.1141 0.1553 0.009 0.948 5.7 103.5 20.6 407 n/a 4_nqh: 0.1141 0.1553 0.009 0.948 5.7 103.5 20.6 407 n/a 4_sol: 0.1133 0.1521 0.009 0.948 5.7 103.5 20.9 436 n/a 4_weight: 0.1133 0.1521 0.009 0.948 5.7 103.5 20.9 436 n/a 4_xyzrec: 0.1120 0.1558 0.010 0.988 5.7 103.5 20.9 436 n/a 4_adp: 0.1108 0.1564 0.010 0.988 5.2 101.2 20.9 436 n/a 4_regHadp: 0.1108 0.1563 0.010 0.988 5.2 101.2 20.9 436 n/a 4_occ: 0.1100 0.1559 0.010 0.988 5.2 101.2 20.9 436 n/a 5_bss: 0.1099 0.1552 0.010 0.988 4.9 100.9 20.6 436 n/a 5_settarget: 0.1099 0.1552 0.010 0.988 4.9 100.9 20.6 436 n/a 5_updatecdl: 0.1099 0.1552 0.010 0.988 4.9 100.9 20.6 436 n/a 5_setrh: 0.1101 0.1551 0.010 0.988 4.9 100.9 20.6 436 n/a 5_nqh: 0.1101 0.1551 0.010 0.988 4.9 100.9 20.6 436 n/a 5_sol: 0.1095 0.1503 0.010 0.988 4.9 100.9 21.1 478 n/a 5_weight: 0.1095 0.1503 0.010 0.988 4.9 100.9 21.1 478 n/a 5_xyzrec: 0.1119 0.1514 0.010 1.008 4.9 100.9 21.1 478 n/a 5_adp: 0.1106 0.1504 0.010 1.008 5.2 100.6 21.2 478 n/a 5_regHadp: 0.1106 0.1503 0.010 1.008 5.2 100.6 21.2 478 n/a 5_occ: 0.1097 0.1505 0.010 1.008 5.2 100.6 21.2 478 n/a end: 0.1097 0.1503 0.010 1.008 4.9 100.4 21.0 478 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2353655_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2353655_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1500 Refinement macro-cycles (run) : 937.7700 Write final files (write_after_run_outputs) : 19.9400 Total : 961.8600 Total CPU time: 16.45 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:28 PST -0800 (1735494088.04 s) Start R-work = 0.1612, R-free = 0.1672 Final R-work = 0.1097, R-free = 0.1503 =============================================================================== Job complete usr+sys time: 1006.52 seconds wall clock time: 17 minutes 9.27 seconds (1029.27 seconds total)