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_8008321.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8008321.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8008321.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 =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.37, per 1000 atoms: 0.41 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: 0.36 Conformation dependent library (CDL) restraints added in 131.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 533 0.92 - 1.17: 1104 1.17 - 1.43: 667 1.43 - 1.69: 824 1.69 - 1.94: 25 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 104 " pdb=" CA ALA A 104 " ideal model delta sigma weight residual 1.455 1.703 -0.248 1.25e-02 6.40e+03 3.95e+02 bond pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 1.246 1.419 -0.173 9.20e-03 1.18e+04 3.52e+02 bond pdb=" N THR A 34 " pdb=" CA THR A 34 " ideal model delta sigma weight residual 1.458 1.241 0.216 1.22e-02 6.72e+03 3.15e+02 bond pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 1.242 1.091 0.151 8.60e-03 1.35e+04 3.07e+02 bond pdb=" C ARG A 98 " pdb=" N ALYS A 99 " ideal model delta sigma weight residual 1.333 1.566 -0.233 1.38e-02 5.25e+03 2.85e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3184 4.72 - 9.43: 1852 9.43 - 14.15: 610 14.15 - 18.87: 118 18.87 - 23.59: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA AGLU A 90 " pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 120.82 137.50 -16.68 1.05e+00 9.07e-01 2.52e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 134.89 -13.54 9.20e-01 1.18e+00 2.17e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 121.53 109.25 12.28 8.70e-01 1.32e+00 1.99e+02 angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.15 106.84 15.31 1.14e+00 7.69e-01 1.80e+02 angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 95.79 13.21 1.00e+00 1.00e+00 1.74e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.44: 1318 18.44 - 36.88: 121 36.88 - 55.31: 30 55.31 - 73.75: 10 73.75 - 92.19: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -141.50 18.90 0 2.50e+00 1.60e-01 5.72e+01 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 122.80 104.37 18.43 0 2.50e+00 1.60e-01 5.43e+01 dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -141.02 18.42 0 2.50e+00 1.60e-01 5.43e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.222: 95 0.222 - 0.440: 77 0.440 - 0.658: 49 0.658 - 0.877: 16 0.877 - 1.095: 6 Chirality restraints: 243 Sorted by residual: 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 3.61 -1.09 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA ALA A 56 " pdb=" N ALA A 56 " pdb=" C ALA A 56 " pdb=" CB ALA A 56 " both_signs ideal model delta sigma weight residual False 2.48 3.48 -1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " 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=" CB PHE A 162 " -0.057 2.00e-02 2.50e+03 7.67e-02 1.77e+02 pdb=" CG PHE A 162 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.076 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.066 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.072 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.098 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.111 2.00e-02 2.50e+03 6.98e-02 1.46e+02 pdb=" CG PHE A 119 " -0.094 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.137 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.022 2.00e-02 2.50e+03 6.61e-02 1.31e+02 pdb=" CG ATYR A 67 " -0.027 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.045 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.083 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.110 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.055 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.016 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 1194 2.34 - 2.90: 8151 2.90 - 3.47: 10475 3.47 - 4.03: 15175 4.03 - 4.60: 21550 Nonbonded interactions: 56545 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.770 2.100 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.792 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.815 2.100 nonbonded pdb=" O ALA A 6 " pdb=" H THR A 34 " model vdw 1.830 2.450 nonbonded pdb=" H CYS A 46 " pdb=" O VAL A 50 " model vdw 1.849 2.450 ... (remaining 56540 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_8008321_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= 0.2793 r_free= 0.1802 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.409792 | | target function (ml) not normalized (work): 71628.251983 | | target function (ml) not normalized (free): 3269.276153 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3198 0.2154 7.5521 5.0309| | 2: 3.63 - 2.88 1.00 2711 122 0.2635 0.1620 4.3261 4.3214| | 3: 2.88 - 2.52 1.00 2682 148 0.2541 0.1755 4.1779 4.1986| | 4: 2.52 - 2.29 1.00 2661 139 0.2562 0.1636 3.5026 3.6918| | 5: 2.29 - 2.13 1.00 2678 122 0.2700 0.1281 3.4143 3.3474| | 6: 2.13 - 2.00 1.00 2692 117 0.2765 0.1852 3.3216 3.4122| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.53 0.77 0.23 1292.06| | 2: 3.63 - 2.88 2711 122 0.83 23.70 1.31 0.23 1292.06| | 3: 2.88 - 2.52 2682 148 0.73 32.80 1.28 0.23 1292.06| | 4: 2.52 - 2.29 2661 139 0.93 11.54 1.30 0.26 137.38| | 5: 2.29 - 2.13 2678 122 0.92 13.85 1.32 0.26 137.38| | 6: 2.13 - 2.00 2692 117 0.90 16.47 1.34 0.26 137.38| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 137.38 max = 1292.06 mean = 721.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 19.32| |phase err.(test): min = 0.00 max = 89.54 mean = 19.45| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.248 1557 Z= 5.441 Angle : 5.290 21.328 2118 Z= 3.740 Chirality : 0.390 1.095 243 Planarity : 0.030 0.100 284 Dihedral : 14.300 92.188 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.27 % 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 (0.48), residues: 224 helix: -2.26 (0.39), residues: 108 sheet: -0.87 (0.87), residues: 28 loop : -0.24 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.019 ARG A 156 TYR 0.064 0.029 TYR A 139 PHE 0.119 0.062 PHE A 164 HIS 0.045 0.027 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= 0.2793 r_free= 0.1802 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.409792 | | target function (ml) not normalized (work): 71628.251983 | | target function (ml) not normalized (free): 3269.276153 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2800 percent. r_work = 0.2921 r_free = 0.1975 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2867 0.2921 0.1975 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2867 0.2921 0.1975 n_refl.: 17050 remove outliers: r(all,work,free)=0.2157 0.2169 0.1975 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2129 0.2140 0.1958 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1611 0.1610 0.1633 n_refl.: 17045 remove outliers: r(all,work,free)=0.1610 0.1609 0.1633 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 0.4016 394.840 363.768 0.655 1.010 0.397 11.894-9.307 99.02 97 4 0.1848 633.730 612.283 0.934 1.012 0.380 9.237-7.194 100.00 213 7 0.2176 518.327 510.321 0.959 1.012 0.371 7.162-5.571 100.00 427 22 0.2303 389.005 375.851 0.930 1.011 0.311 5.546-4.326 100.00 867 58 0.1396 534.042 527.957 0.962 1.009 0.230 4.315-3.360 100.00 1859 96 0.1300 507.879 503.753 1.019 1.005 0.212 3.356-2.611 100.00 3867 181 0.1638 333.648 328.999 1.011 1.000 0.019 2.608-2.000 99.99 8818 434 0.1649 217.481 213.432 1.032 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4940 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1609 r_free=0.1633 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=0.1609 r_free=0.1636 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.229571 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.880210 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 0.1355 0.1648 0.0293 0.009 1.0 1.0 0.5 0.0 0 11.615 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.55 16.48 2.93 3.013 18.441 0.880 0.023 12.82 16.71 3.88 3.618 18.688 0.880 0.021 Individual atomic B min max mean iso aniso Overall: 6.28 113.88 19.94 4.09 1785 0 Protein: 6.28 112.97 17.18 4.09 1519 0 Water: 8.76 113.88 35.97 N/A 258 0 Other: 21.89 36.82 26.42 N/A 8 0 Chain A: 6.28 113.88 19.94 N/A 1785 0 Histogram: Values Number of atoms 6.28 - 17.04 1086 17.04 - 27.80 345 27.80 - 38.56 182 38.56 - 49.32 96 49.32 - 60.08 49 60.08 - 70.84 13 70.84 - 81.60 6 81.60 - 92.36 4 92.36 - 103.12 1 103.12 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1282 r_free=0.1671 r_work=0.1285 r_free=0.1677 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1285 r_free = 0.1677 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1280 r_free = 0.1666 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.27 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= 0.1280 r_free= 0.1666 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020193 | | target function (ls_wunit_k1) not normalized (work): 327.874210 | | target function (ls_wunit_k1) not normalized (free): 27.582685 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1299 0.1280 0.1666 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1917 0.1916 0.1986 n_refl.: 17044 remove outliers: r(all,work,free)=0.1917 0.1916 0.1986 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1888 0.1887 0.1970 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1298 0.1280 0.1659 n_refl.: 17044 remove outliers: r(all,work,free)=0.1297 0.1278 0.1659 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 0.3526 303.926 278.926 0.628 1.010 0.369 11.894-9.307 99.02 97 4 0.1669 488.817 479.590 0.921 1.010 0.368 9.237-7.194 100.00 213 7 0.1834 399.803 396.921 0.960 1.010 0.354 7.162-5.571 100.00 427 22 0.1831 300.053 295.190 0.931 1.009 0.301 5.546-4.326 100.00 867 58 0.1057 411.924 409.634 0.959 1.008 0.215 4.315-3.360 100.00 1859 96 0.0937 391.744 391.410 1.017 1.005 0.201 3.356-2.611 100.00 3867 181 0.1304 257.353 255.973 1.014 1.000 0.071 2.608-2.000 99.99 8818 434 0.1350 167.750 166.225 1.023 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3817 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1659 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1278 r_free=0.1659 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1659 | n_water=258 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1285 r_free=0.1645 | n_water=254 | time (s): 20.950 (total time: 21.870) Filter (q & B) r_work=0.1285 r_free=0.1646 | n_water=252 | time (s): 1.640 (total time: 23.510) Compute maps r_work=0.1285 r_free=0.1646 | n_water=252 | time (s): 0.580 (total time: 24.090) Filter (map) r_work=0.1320 r_free=0.1627 | n_water=208 | time (s): 2.210 (total time: 26.300) Find peaks r_work=0.1320 r_free=0.1627 | n_water=208 | time (s): 0.670 (total time: 26.970) Add new water r_work=0.1548 r_free=0.1864 | n_water=363 | time (s): 1.670 (total time: 28.640) Refine new water occ: r_work=0.1344 r_free=0.1635 adp: r_work=0.1281 r_free=0.1626 occ: r_work=0.1286 r_free=0.1604 adp: r_work=0.1253 r_free=0.1604 occ: r_work=0.1255 r_free=0.1603 adp: r_work=0.1243 r_free=0.1601 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1601 r_work=0.1243 r_free=0.1601 | n_water=363 | time (s): 11.260 (total time: 39.900) Filter (q & B) r_work=0.1245 r_free=0.1606 | n_water=355 | time (s): 2.090 (total time: 41.990) Filter (dist only) r_work=0.1246 r_free=0.1609 | n_water=354 | time (s): 26.760 (total time: 68.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.241538 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.035763 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 0.1217 0.1598 0.0380 0.008 0.9 2.2 0.5 0.0 0 12.121 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.17 15.98 3.80 4.175 20.969 1.036 0.018 11.97 16.08 4.11 4.313 21.298 1.036 0.018 Individual atomic B min max mean iso aniso Overall: 6.92 107.58 21.33 4.45 1881 0 Protein: 6.92 107.58 17.77 4.42 1519 0 Water: 8.60 67.46 36.23 N/A 354 0 Other: 26.46 48.17 37.18 N/A 8 0 Chain A: 6.92 107.58 19.48 N/A 1735 0 Chain S: 17.10 67.46 43.29 N/A 146 0 Histogram: Values Number of atoms 6.92 - 16.99 1045 16.99 - 27.05 359 27.05 - 37.12 217 37.12 - 47.18 154 47.18 - 57.25 71 57.25 - 67.32 22 67.32 - 77.38 5 77.38 - 87.45 5 87.45 - 97.52 1 97.52 - 107.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1608 r_work=0.1199 r_free=0.1608 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1608 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1615 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 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= 0.1198 r_free= 0.1615 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017109 | | target function (ls_wunit_k1) not normalized (work): 277.769166 | | target function (ls_wunit_k1) not normalized (free): 24.964031 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1198 0.1615 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1765 0.1759 0.1925 n_refl.: 17042 remove outliers: r(all,work,free)=0.1765 0.1759 0.1925 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1741 0.1735 0.1909 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1191 0.1606 n_refl.: 17042 remove outliers: r(all,work,free)=0.1210 0.1190 0.1606 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 0.3206 300.759 285.562 0.606 1.005 0.350 11.894-9.307 99.02 97 4 0.1492 488.817 485.974 0.917 1.006 0.340 9.237-7.194 100.00 213 7 0.1652 399.803 400.524 0.977 1.006 0.285 7.162-5.571 100.00 427 22 0.1526 300.053 296.695 0.931 1.005 0.271 5.546-4.326 100.00 867 58 0.0884 411.924 409.164 0.960 1.004 0.216 4.315-3.360 100.00 1859 96 0.0845 391.744 391.027 1.015 1.003 0.211 3.356-2.611 100.00 3867 181 0.1195 257.353 256.537 1.010 1.001 0.111 2.608-2.000 99.99 8818 434 0.1330 167.750 166.752 1.016 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3264 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1606 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1191 r_free=0.1608 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1608 | n_water=354 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1191 r_free=0.1608 | n_water=354 | time (s): 26.480 (total time: 27.100) Filter (q & B) r_work=0.1191 r_free=0.1608 | n_water=354 | time (s): 0.900 (total time: 28.000) Compute maps r_work=0.1191 r_free=0.1608 | n_water=354 | time (s): 0.580 (total time: 28.580) Filter (map) r_work=0.1256 r_free=0.1631 | n_water=258 | time (s): 1.560 (total time: 30.140) Find peaks r_work=0.1256 r_free=0.1631 | n_water=258 | time (s): 0.470 (total time: 30.610) Add new water r_work=0.1446 r_free=0.1803 | n_water=403 | time (s): 1.390 (total time: 32.000) Refine new water occ: r_work=0.1247 r_free=0.1567 adp: r_work=0.1240 r_free=0.1570 occ: r_work=0.1221 r_free=0.1538 adp: r_work=0.1211 r_free=0.1542 occ: r_work=0.1200 r_free=0.1521 adp: r_work=0.1192 r_free=0.1524 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1524 r_work=0.1192 r_free=0.1524 | n_water=403 | time (s): 28.410 (total time: 60.410) Filter (q & B) r_work=0.1195 r_free=0.1535 | n_water=393 | time (s): 1.810 (total time: 62.220) Filter (dist only) r_work=0.1195 r_free=0.1535 | n_water=393 | time (s): 30.220 (total time: 92.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.944818 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.175572 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 0.1172 0.1554 0.0382 0.009 1.0 3.8 0.5 0.0 0 0.972 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.72 15.54 3.82 4.439 21.555 0.176 4.998 11.51 15.71 4.19 5.008 21.426 0.176 4.978 Individual atomic B min max mean iso aniso Overall: 6.35 105.16 20.76 4.80 1920 0 Protein: 6.35 105.16 16.96 4.79 1519 0 Water: 8.19 63.69 35.08 N/A 393 0 Other: 28.71 50.39 37.89 N/A 8 0 Chain A: 6.35 105.16 18.71 N/A 1732 0 Chain S: 14.53 63.69 39.61 N/A 188 0 Histogram: Values Number of atoms 6.35 - 16.23 1078 16.23 - 26.12 342 26.12 - 36.00 216 36.00 - 45.88 169 45.88 - 55.76 72 55.76 - 65.64 29 65.64 - 75.52 6 75.52 - 85.40 3 85.40 - 95.28 3 95.28 - 105.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1571 r_work=0.1152 r_free=0.1571 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1152 r_free = 0.1571 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1560 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.16 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= 0.1143 r_free= 0.1560 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.973659 | | target function (ml) not normalized (work): 80742.374431 | | target function (ml) not normalized (free): 4193.063944 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1163 0.1143 0.1560 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1674 0.1665 0.1894 n_refl.: 17041 remove outliers: r(all,work,free)=0.1674 0.1665 0.1894 n_refl.: 17041 overall B=-0.47 to atoms: r(all,work,free)=0.1643 0.1633 0.1879 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1162 0.1142 0.1558 n_refl.: 17041 remove outliers: r(all,work,free)=0.1162 0.1142 0.1558 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 0.3496 300.759 278.986 0.568 1.003 0.340 11.894-9.307 99.02 97 4 0.1728 488.817 484.353 0.920 1.004 0.340 9.237-7.194 100.00 213 7 0.1783 399.803 399.008 0.990 1.004 0.275 7.162-5.571 100.00 427 22 0.1629 300.053 295.472 0.942 1.004 0.251 5.546-4.326 100.00 867 58 0.0932 411.924 408.286 0.966 1.004 0.211 4.315-3.360 100.00 1859 96 0.0875 391.744 389.737 1.013 1.003 0.212 3.356-2.611 100.00 3867 181 0.1277 257.353 255.227 1.010 1.001 0.132 2.608-2.000 99.99 8818 434 0.1095 167.750 166.335 1.009 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1723 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1558 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=0.1555 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1555 | n_water=393 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1144 r_free=0.1555 | n_water=393 | time (s): 31.380 (total time: 32.030) Filter (q & B) r_work=0.1144 r_free=0.1555 | n_water=392 | time (s): 1.840 (total time: 33.870) Compute maps r_work=0.1144 r_free=0.1555 | n_water=392 | time (s): 0.570 (total time: 34.440) Filter (map) r_work=0.1198 r_free=0.1584 | n_water=302 | time (s): 2.000 (total time: 36.440) Find peaks r_work=0.1198 r_free=0.1584 | n_water=302 | time (s): 0.460 (total time: 36.900) Add new water r_work=0.1362 r_free=0.1706 | n_water=441 | time (s): 1.790 (total time: 38.690) Refine new water occ: r_work=0.1184 r_free=0.1536 adp: r_work=0.1174 r_free=0.1538 occ: r_work=0.1158 r_free=0.1525 adp: r_work=0.1147 r_free=0.1524 occ: r_work=0.1140 r_free=0.1516 adp: r_work=0.1131 r_free=0.1517 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1517 r_work=0.1131 r_free=0.1517 | n_water=441 | time (s): 36.000 (total time: 74.690) Filter (q & B) r_work=0.1133 r_free=0.1525 | n_water=433 | time (s): 1.770 (total time: 76.460) Filter (dist only) r_work=0.1133 r_free=0.1525 | n_water=433 | time (s): 33.790 (total time: 110.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.023371 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.170004 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 0.1121 0.1573 0.0453 0.010 1.0 4.8 0.5 0.0 0 1.012 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 15.73 4.53 4.562 20.961 0.170 4.966 11.12 15.66 4.54 4.764 20.941 0.170 4.958 Individual atomic B min max mean iso aniso Overall: 5.33 102.51 20.74 4.92 1960 0 Protein: 5.33 102.51 16.40 4.90 1519 0 Water: 8.33 63.97 35.67 N/A 433 0 Other: 27.89 49.66 36.22 N/A 8 0 Chain A: 5.33 102.51 18.09 N/A 1732 0 Chain S: 17.05 63.97 40.87 N/A 228 0 Histogram: Values Number of atoms 5.33 - 15.05 1015 15.05 - 24.77 384 24.77 - 34.49 224 34.49 - 44.20 186 44.20 - 53.92 102 53.92 - 63.64 34 63.64 - 73.36 6 73.36 - 83.07 3 83.07 - 92.79 4 92.79 - 102.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1566 r_work=0.1112 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1567 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1578 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.01 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= 0.1104 r_free= 0.1578 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.957142 | | target function (ml) not normalized (work): 80474.247152 | | target function (ml) not normalized (free): 4197.422125 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1127 0.1104 0.1578 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1587 0.1573 0.1888 n_refl.: 17041 remove outliers: r(all,work,free)=0.1587 0.1573 0.1888 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1571 0.1557 0.1881 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1125 0.1102 0.1575 n_refl.: 17041 remove outliers: r(all,work,free)=0.1125 0.1102 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 0.3656 300.759 282.023 0.561 1.000 0.324 11.894-9.307 99.02 97 4 0.1707 488.817 483.308 0.925 1.001 0.314 9.237-7.194 100.00 213 7 0.1742 399.803 400.288 0.994 1.002 0.250 7.162-5.571 100.00 427 22 0.1546 300.053 293.900 0.939 1.002 0.210 5.546-4.326 100.00 867 58 0.0893 411.924 408.279 0.966 1.002 0.201 4.315-3.360 100.00 1859 96 0.0860 391.744 389.468 1.007 1.002 0.201 3.356-2.611 100.00 3867 181 0.1231 257.353 255.076 1.002 1.001 0.131 2.608-2.000 99.99 8818 434 0.1045 167.750 166.614 0.995 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9177 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1102 r_free=0.1575 After: r_work=0.1104 r_free=0.1574 ================================== NQH flips ================================== r_work=0.1104 r_free=0.1574 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1104 r_free=0.1574 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1104 r_free=0.1574 | n_water=433 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1104 r_free=0.1574 | n_water=433 | time (s): 34.540 (total time: 35.440) Filter (q & B) r_work=0.1104 r_free=0.1574 | n_water=432 | time (s): 2.120 (total time: 37.560) Compute maps r_work=0.1104 r_free=0.1574 | n_water=432 | time (s): 0.740 (total time: 38.300) Filter (map) r_work=0.1176 r_free=0.1577 | n_water=333 | time (s): 1.720 (total time: 40.020) Find peaks r_work=0.1176 r_free=0.1577 | n_water=333 | time (s): 0.520 (total time: 40.540) Add new water r_work=0.1298 r_free=0.1675 | n_water=464 | time (s): 2.000 (total time: 42.540) Refine new water occ: r_work=0.1147 r_free=0.1516 adp: r_work=0.1139 r_free=0.1528 occ: r_work=0.1128 r_free=0.1502 adp: r_work=0.1118 r_free=0.1511 occ: r_work=0.1115 r_free=0.1496 adp: r_work=0.1107 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1107 r_free=0.1501 r_work=0.1107 r_free=0.1501 | n_water=464 | time (s): 32.410 (total time: 74.950) Filter (q & B) r_work=0.1110 r_free=0.1510 | n_water=456 | time (s): 1.720 (total time: 76.670) Filter (dist only) r_work=0.1113 r_free=0.1510 | n_water=455 | time (s): 37.490 (total time: 114.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.919849 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164028 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 0.1133 0.1511 0.0378 0.010 1.0 3.8 0.5 0.0 0 0.960 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 15.11 3.78 4.577 20.667 0.164 4.955 11.22 15.07 3.85 4.648 20.761 0.164 4.944 Individual atomic B min max mean iso aniso Overall: 5.08 101.05 20.81 5.02 1982 0 Protein: 5.08 101.05 16.15 4.99 1519 0 Water: 7.57 67.63 36.14 N/A 455 0 Other: 27.73 49.24 35.58 N/A 8 0 Chain A: 5.08 101.05 17.80 N/A 1731 0 Chain S: 16.55 67.63 41.59 N/A 251 0 Histogram: Values Number of atoms 5.08 - 14.68 1012 14.68 - 24.28 380 24.28 - 33.87 222 33.87 - 43.47 180 43.47 - 53.07 131 53.07 - 62.66 39 62.66 - 72.26 7 72.26 - 81.86 4 81.86 - 91.45 3 91.45 - 101.05 4 =========================== Idealize ADP of riding H ========================== r_work=0.1122 r_free=0.1507 r_work=0.1122 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1122 r_free = 0.1507 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1116 r_free = 0.1505 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1116 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.939067 | | target function (ml) not normalized (work): 80180.808751 | | target function (ml) not normalized (free): 4159.671478 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1135 0.1335 5.4828 5.6414| | 2: 3.63 - 2.88 1.00 2711 122 0.1095 0.1515 5.2213 5.3644| | 3: 2.88 - 2.52 1.00 2681 148 0.1359 0.1776 5.1299 5.2145| | 4: 2.52 - 2.29 1.00 2661 139 0.0947 0.1463 4.6238 4.918| | 5: 2.29 - 2.13 1.00 2678 122 0.0973 0.1485 4.5746 4.8794| | 6: 2.13 - 2.00 1.00 2692 117 0.1122 0.1742 4.5712 4.7659| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.02 1.00 0.96 6337.21| | 2: 3.63 - 2.88 2711 122 0.92 12.79 1.01 0.96 6337.21| | 3: 2.88 - 2.52 2681 148 0.88 18.91 0.99 0.96 6337.21| | 4: 2.52 - 2.29 2661 139 0.93 11.91 1.01 0.98 2068.85| | 5: 2.29 - 2.13 2678 122 0.92 13.91 1.00 0.98 2068.85| | 6: 2.13 - 2.00 2692 117 0.90 16.54 0.99 0.98 2068.85| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2068.85 max = 6337.21 mean = 4225.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 90.00 mean = 13.81| |phase err.(test): min = 0.00 max = 87.32 mean = 13.37| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1116 0.1505 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1584 0.1574 0.1802 n_refl.: 17041 remove outliers: r(all,work,free)=0.1584 0.1574 0.1802 n_refl.: 17041 overall B=-0.22 to atoms: r(all,work,free)=0.1571 0.1561 0.1796 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1115 0.1503 n_refl.: 17041 remove outliers: r(all,work,free)=0.1133 0.1114 0.1503 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 0.3650 297.188 280.726 0.553 1.006 0.340 11.894-9.307 99.02 97 4 0.1772 488.817 482.313 0.915 1.007 0.320 9.237-7.194 100.00 213 7 0.1805 399.803 401.266 0.986 1.007 0.240 7.162-5.571 100.00 427 22 0.1613 300.053 292.904 0.927 1.007 0.220 5.546-4.326 100.00 867 58 0.0923 411.924 408.902 0.961 1.006 0.200 4.315-3.360 100.00 1859 96 0.0877 391.744 389.822 1.003 1.003 0.201 3.356-2.611 100.00 3867 181 0.1241 257.353 255.109 1.001 1.000 0.048 2.608-2.000 99.99 8818 434 0.1044 167.750 166.376 0.994 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.7631 ================= 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 : 0.2793 0.1802 0.080 5.290 8.8 119.3 19.9 258 0.000 1_bss: 0.1609 0.1633 0.080 5.290 8.4 118.9 19.5 258 0.000 1_settarget: 0.1609 0.1633 0.080 5.290 8.4 118.9 19.5 258 0.000 1_nqh: 0.1609 0.1636 0.080 5.290 8.4 118.9 19.5 258 0.003 1_weight: 0.1609 0.1636 0.080 5.290 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1355 0.1648 0.009 0.985 8.4 118.9 19.5 258 0.142 1_adp: 0.1282 0.1671 0.009 0.985 6.3 113.9 19.9 258 0.142 1_regHadp: 0.1285 0.1677 0.009 0.985 6.3 113.9 19.9 258 0.142 1_occ: 0.1280 0.1666 0.009 0.985 6.3 113.9 19.9 258 0.142 2_bss: 0.1278 0.1659 0.009 0.985 5.9 113.5 19.5 258 0.142 2_settarget: 0.1278 0.1659 0.009 0.985 5.9 113.5 19.5 258 0.142 2_updatecdl: 0.1278 0.1659 0.009 0.996 5.9 113.5 19.5 258 0.142 2_nqh: 0.1278 0.1659 0.009 0.996 5.9 113.5 19.5 258 0.142 2_sol: 0.1246 0.1609 0.009 0.996 5.9 112.6 20.7 354 n/a 2_weight: 0.1246 0.1609 0.009 0.996 5.9 112.6 20.7 354 n/a 2_xyzrec: 0.1217 0.1598 0.008 0.930 5.9 112.6 20.7 354 n/a 2_adp: 0.1197 0.1608 0.008 0.930 6.9 107.6 21.3 354 n/a 2_regHadp: 0.1199 0.1608 0.008 0.930 6.9 107.6 21.3 354 n/a 2_occ: 0.1198 0.1615 0.008 0.930 6.9 107.6 21.3 354 n/a 3_bss: 0.1190 0.1606 0.008 0.930 6.5 107.2 21.0 354 n/a 3_settarget: 0.1190 0.1606 0.008 0.930 6.5 107.2 21.0 354 n/a 3_updatecdl: 0.1190 0.1606 0.008 0.928 6.5 107.2 21.0 354 n/a 3_nqh: 0.1191 0.1608 0.008 0.928 6.5 107.2 21.0 354 n/a 3_sol: 0.1195 0.1535 0.008 0.928 6.5 107.2 21.0 393 n/a 3_weight: 0.1195 0.1535 0.008 0.928 6.5 107.2 21.0 393 n/a 3_xyzrec: 0.1172 0.1554 0.009 0.983 6.5 107.2 21.0 393 n/a 3_adp: 0.1151 0.1571 0.009 0.983 6.4 105.2 20.8 393 n/a 3_regHadp: 0.1152 0.1571 0.009 0.983 6.4 105.2 20.8 393 n/a 3_occ: 0.1143 0.1560 0.009 0.983 6.4 105.2 20.8 393 n/a 4_bss: 0.1142 0.1558 0.009 0.983 5.9 104.7 20.3 393 n/a 4_settarget: 0.1142 0.1558 0.009 0.983 5.9 104.7 20.3 393 n/a 4_updatecdl: 0.1142 0.1558 0.009 0.982 5.9 104.7 20.3 393 n/a 4_nqh: 0.1144 0.1555 0.009 0.982 5.9 104.7 20.3 393 n/a 4_sol: 0.1133 0.1525 0.009 0.982 5.9 104.7 20.8 433 n/a 4_weight: 0.1133 0.1525 0.009 0.982 5.9 104.7 20.8 433 n/a 4_xyzrec: 0.1121 0.1573 0.010 0.989 5.9 104.7 20.8 433 n/a 4_adp: 0.1112 0.1566 0.010 0.989 5.3 102.5 20.7 433 n/a 4_regHadp: 0.1112 0.1567 0.010 0.989 5.3 102.5 20.7 433 n/a 4_occ: 0.1104 0.1578 0.010 0.989 5.3 102.5 20.7 433 n/a 5_bss: 0.1102 0.1575 0.010 0.989 5.1 102.2 20.5 433 n/a 5_settarget: 0.1102 0.1575 0.010 0.989 5.1 102.2 20.5 433 n/a 5_updatecdl: 0.1102 0.1575 0.010 0.989 5.1 102.2 20.5 433 n/a 5_setrh: 0.1104 0.1574 0.010 0.989 5.1 102.2 20.5 433 n/a 5_nqh: 0.1104 0.1574 0.010 0.989 5.1 102.2 20.5 433 n/a 5_sol: 0.1113 0.1510 0.010 0.989 5.1 102.2 20.6 455 n/a 5_weight: 0.1113 0.1510 0.010 0.989 5.1 102.2 20.6 455 n/a 5_xyzrec: 0.1133 0.1511 0.010 1.041 5.1 102.2 20.6 455 n/a 5_adp: 0.1122 0.1507 0.010 1.041 5.1 101.0 20.8 455 n/a 5_regHadp: 0.1122 0.1507 0.010 1.041 5.1 101.0 20.8 455 n/a 5_occ: 0.1116 0.1505 0.010 1.041 5.1 101.0 20.8 455 n/a end: 0.1114 0.1503 0.010 1.041 4.9 100.8 20.6 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8008321_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8008321_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.4000 Refinement macro-cycles (run) : 920.1500 Write final files (write_after_run_outputs) : 23.0100 Total : 947.5600 Total CPU time: 16.20 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:12 PST -0800 (1735494072.85 s) Start R-work = 0.1609, R-free = 0.1633 Final R-work = 0.1114, R-free = 0.1503 =============================================================================== Job complete usr+sys time: 994.32 seconds wall clock time: 16 minutes 57.08 seconds (1017.08 seconds total)