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_8954467.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8954467.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8954467.pdb" 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" } 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: 1.98, per 1000 atoms: 0.59 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 140.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.93: 641 0.93 - 1.18: 1015 1.18 - 1.43: 645 1.43 - 1.68: 820 1.68 - 1.93: 32 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.444 1.645 -0.201 1.06e-02 8.90e+03 3.60e+02 bond pdb=" CA ILE A 117 " pdb=" CB ILE A 117 " ideal model delta sigma weight residual 1.542 1.779 -0.237 1.26e-02 6.30e+03 3.54e+02 bond pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 1.232 1.384 -0.152 8.20e-03 1.49e+04 3.42e+02 bond pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 1.524 1.749 -0.225 1.24e-02 6.50e+03 3.29e+02 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.458 1.663 -0.205 1.18e-02 7.18e+03 3.02e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3324 4.88 - 9.75: 1797 9.75 - 14.63: 571 14.63 - 19.51: 78 19.51 - 24.39: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 107.17 15.43 1.00e+00 1.00e+00 2.38e+02 angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.43 111.66 11.77 8.50e-01 1.38e+00 1.92e+02 angle pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " ideal model delta sigma weight residual 115.67 99.67 16.00 1.23e+00 6.61e-01 1.69e+02 angle pdb=" O ILE A 9 " pdb=" C ILE A 9 " pdb=" N LEU A 10 " ideal model delta sigma weight residual 122.94 138.67 -15.73 1.22e+00 6.72e-01 1.66e+02 angle pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" O ALYS A 99 " ideal model delta sigma weight residual 121.65 136.61 -14.96 1.17e+00 7.31e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 1304 17.15 - 34.31: 131 34.31 - 51.46: 33 51.46 - 68.61: 9 68.61 - 85.76: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C HIS A 115 " pdb=" N HIS A 115 " pdb=" CA HIS A 115 " pdb=" CB HIS A 115 " ideal model delta harmonic sigma weight residual -122.60 -146.76 24.16 0 2.50e+00 1.60e-01 9.34e+01 dihedral pdb=" N HIS A 115 " pdb=" C HIS A 115 " pdb=" CA HIS A 115 " pdb=" CB HIS A 115 " ideal model delta harmonic sigma weight residual 122.80 144.93 -22.13 0 2.50e+00 1.60e-01 7.83e+01 dihedral pdb=" N LEU A 187 " pdb=" C LEU A 187 " pdb=" CA LEU A 187 " pdb=" CB LEU A 187 " ideal model delta harmonic sigma weight residual 122.80 144.66 -21.86 0 2.50e+00 1.60e-01 7.64e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.009 - 0.244: 117 0.244 - 0.480: 77 0.480 - 0.715: 34 0.715 - 0.950: 12 0.950 - 1.185: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA HIS A 115 " pdb=" N HIS A 115 " pdb=" C HIS A 115 " pdb=" CB HIS A 115 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.51e+01 chirality pdb=" CA LEU A 187 " pdb=" N LEU A 187 " pdb=" C LEU A 187 " pdb=" CB LEU A 187 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 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 " -0.051 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG PHE A 162 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.125 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.044 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.046 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 5.52e-02 9.14e+01 pdb=" CG PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.135 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.048 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.050 2.00e-02 2.50e+03 5.51e-02 9.09e+01 pdb=" CG BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.095 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.121 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1413 2.37 - 2.93: 8349 2.93 - 3.48: 10433 3.48 - 4.04: 15097 4.04 - 4.60: 21277 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.811 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.826 2.450 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.840 2.270 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.860 2.100 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.873 2.270 ... (remaining 56564 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_8954467_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= 0.2787 r_free= 0.1786 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.424013 | | target function (ml) not normalized (work): 71859.246544 | | target function (ml) not normalized (free): 3252.428063 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3209 0.2031 7.6893 5.0058| | 2: 3.63 - 2.88 1.00 2711 122 0.2637 0.1758 4.3145 4.3224| | 3: 2.88 - 2.52 1.00 2682 148 0.2557 0.1710 4.1674 4.1719| | 4: 2.52 - 2.29 1.00 2661 139 0.2547 0.1557 3.5227 3.5896| | 5: 2.29 - 2.13 1.00 2678 122 0.2628 0.1491 3.3866 3.4445| | 6: 2.13 - 2.00 1.00 2692 117 0.2746 0.1779 3.2936 3.3552| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.17 0.77 0.23 1256.22| | 2: 3.63 - 2.88 2711 122 0.83 23.36 1.31 0.23 1256.22| | 3: 2.88 - 2.52 2682 148 0.74 32.28 1.28 0.23 1256.22| | 4: 2.52 - 2.29 2661 139 0.94 10.92 1.29 0.26 129.43| | 5: 2.29 - 2.13 2678 122 0.92 13.07 1.31 0.26 129.43| | 6: 2.13 - 2.00 2692 117 0.90 15.94 1.34 0.26 129.43| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 129.43 max = 1256.22 mean = 699.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.83 mean = 18.80| |phase err.(test): min = 0.00 max = 89.09 mean = 19.05| |-----------------------------------------------------------------------------| ----------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 0.237 1557 Z= 5.365 Angle : 5.131 15.998 2118 Z= 3.654 Chirality : 0.383 1.185 243 Planarity : 0.034 0.111 284 Dihedral : 13.667 85.762 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 33.51 % 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: -2.82 (0.46), residues: 224 helix: -2.43 (0.37), residues: 109 sheet: -0.72 (0.87), residues: 28 loop : -1.20 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.116 0.021 ARG A 28 TYR 0.068 0.032 TYR A 139 PHE 0.113 0.037 PHE A 164 HIS 0.045 0.020 HIS A 126 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= 0.2787 r_free= 0.1786 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.424013 | | target function (ml) not normalized (work): 71859.246544 | | target function (ml) not normalized (free): 3252.428063 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3208 percent. r_work = 0.2920 r_free = 0.1952 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2920 0.1952 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2920 0.1952 n_refl.: 17050 remove outliers: r(all,work,free)=0.2159 0.2172 0.1952 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2133 0.2145 0.1935 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1620 0.1618 0.1660 n_refl.: 17045 remove outliers: r(all,work,free)=0.1618 0.1616 0.1660 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3935 398.926 360.356 0.658 1.019 0.409 11.894-9.307 99.02 97 4 0.1861 633.589 615.900 0.922 1.020 0.390 9.237-7.194 100.00 213 7 0.2195 518.212 507.439 0.939 1.019 0.381 7.162-5.571 100.00 427 22 0.2341 388.919 375.841 0.911 1.017 0.298 5.546-4.326 100.00 867 58 0.1398 533.923 528.363 0.959 1.014 0.241 4.315-3.360 100.00 1859 96 0.1292 507.766 503.554 1.013 1.008 0.181 3.356-2.611 100.00 3867 181 0.1670 333.573 328.850 1.011 0.999 0.091 2.608-2.000 99.99 8818 434 0.1646 217.433 213.578 1.034 0.982 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3821 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1616 r_free=0.1660 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=0.1617 r_free=0.1662 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.927648 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.858413 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 0.1349 0.1645 0.0296 0.009 1.0 1.3 0.5 0.0 0 11.964 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.45 2.96 3.013 18.471 0.858 0.023 12.78 16.65 3.87 3.590 18.696 0.858 0.020 Individual atomic B min max mean iso aniso Overall: 6.10 113.91 19.93 4.07 1785 0 Protein: 6.10 112.76 17.17 4.07 1519 0 Water: 8.58 113.91 35.97 N/A 258 0 Other: 21.76 36.54 26.14 N/A 8 0 Chain A: 6.10 113.91 19.93 N/A 1785 0 Histogram: Values Number of atoms 6.10 - 16.88 1083 16.88 - 27.66 345 27.66 - 38.44 185 38.44 - 49.22 94 49.22 - 60.00 49 60.00 - 70.79 14 70.79 - 81.57 7 81.57 - 92.35 4 92.35 - 103.13 1 103.13 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1665 r_work=0.1281 r_free=0.1672 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1672 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1277 r_free = 0.1666 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1277 r_free= 0.1666 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020028 | | target function (ls_wunit_k1) not normalized (work): 325.177498 | | target function (ls_wunit_k1) not normalized (free): 27.601986 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1277 0.1666 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1903 0.1901 0.1995 n_refl.: 17043 remove outliers: r(all,work,free)=0.1903 0.1901 0.1995 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1866 0.1864 0.1973 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1276 0.1658 n_refl.: 17043 remove outliers: r(all,work,free)=0.1292 0.1274 0.1658 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 0.3444 306.525 281.175 0.631 1.006 0.370 11.894-9.307 99.02 97 4 0.1714 487.726 476.176 0.919 1.007 0.370 9.237-7.194 100.00 213 7 0.1833 398.911 395.127 0.958 1.007 0.351 7.162-5.571 100.00 427 22 0.1878 299.383 293.478 0.926 1.006 0.259 5.546-4.326 100.00 867 58 0.1048 411.005 408.303 0.960 1.006 0.221 4.315-3.360 100.00 1859 96 0.0925 390.870 390.384 1.016 1.004 0.182 3.356-2.611 100.00 3867 181 0.1295 256.779 255.491 1.010 1.001 0.102 2.608-2.000 99.99 8818 434 0.1348 167.376 166.072 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1625 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1658 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1658 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1658 | n_water=258 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1279 r_free=0.1649 | n_water=254 | time (s): 19.890 (total time: 20.600) Filter (q & B) r_work=0.1279 r_free=0.1650 | n_water=252 | time (s): 1.760 (total time: 22.360) Compute maps r_work=0.1279 r_free=0.1650 | n_water=252 | time (s): 0.560 (total time: 22.920) Filter (map) r_work=0.1318 r_free=0.1646 | n_water=209 | time (s): 1.620 (total time: 24.540) Find peaks r_work=0.1318 r_free=0.1646 | n_water=209 | time (s): 0.660 (total time: 25.200) Add new water r_work=0.1533 r_free=0.1864 | n_water=368 | time (s): 1.680 (total time: 26.880) Refine new water occ: r_work=0.1327 r_free=0.1590 adp: r_work=0.1269 r_free=0.1589 occ: r_work=0.1274 r_free=0.1563 adp: r_work=0.1242 r_free=0.1569 occ: r_work=0.1243 r_free=0.1554 adp: r_work=0.1233 r_free=0.1558 ADP+occupancy (water only), MIN, final r_work=0.1233 r_free=0.1558 r_work=0.1233 r_free=0.1558 | n_water=368 | time (s): 20.940 (total time: 47.820) Filter (q & B) r_work=0.1235 r_free=0.1567 | n_water=358 | time (s): 1.590 (total time: 49.410) Filter (dist only) r_work=0.1236 r_free=0.1569 | n_water=357 | time (s): 28.390 (total time: 77.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.811993 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.001495 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 0.1211 0.1603 0.0392 0.008 0.9 2.9 0.5 0.0 0 12.406 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 16.03 3.92 4.162 20.797 1.001 0.018 11.96 16.07 4.11 4.180 21.033 1.001 0.018 Individual atomic B min max mean iso aniso Overall: 6.55 107.25 20.96 4.24 1884 0 Protein: 6.55 107.25 17.49 4.23 1519 0 Water: 8.63 65.68 35.49 N/A 357 0 Other: 23.67 42.33 32.84 N/A 8 0 Chain A: 6.55 107.25 19.16 N/A 1736 0 Chain S: 16.67 65.29 42.14 N/A 148 0 Histogram: Values Number of atoms 6.55 - 16.62 1041 16.62 - 26.69 372 26.69 - 36.76 211 36.76 - 46.83 161 46.83 - 56.90 63 56.90 - 66.97 26 66.97 - 77.04 3 77.04 - 87.11 3 87.11 - 97.18 2 97.18 - 107.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1607 r_work=0.1197 r_free=0.1608 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1608 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1608 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.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1193 r_free= 0.1608 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017053 | | target function (ls_wunit_k1) not normalized (work): 276.840203 | | target function (ls_wunit_k1) not normalized (free): 24.646314 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1193 0.1608 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1718 0.1709 0.1932 n_refl.: 17041 remove outliers: r(all,work,free)=0.1718 0.1709 0.1932 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1695 0.1686 0.1917 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1190 0.1603 n_refl.: 17041 remove outliers: r(all,work,free)=0.1210 0.1190 0.1603 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 0.3363 306.525 285.039 0.603 1.007 0.350 11.894-9.307 99.02 97 4 0.1512 487.726 484.491 0.916 1.007 0.350 9.237-7.194 100.00 213 7 0.1707 398.911 398.833 0.974 1.007 0.300 7.162-5.571 100.00 427 22 0.1561 299.383 296.103 0.932 1.007 0.251 5.546-4.326 100.00 867 58 0.0866 411.005 408.273 0.959 1.006 0.206 4.315-3.360 100.00 1859 96 0.0837 390.870 390.264 1.015 1.004 0.201 3.356-2.611 100.00 3867 181 0.1198 256.779 256.025 1.010 1.001 0.111 2.608-2.000 99.99 8818 434 0.1326 167.376 166.366 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1507 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1603 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1603 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1603 | n_water=357 | time (s): 0.790 (total time: 0.790) Filter (dist) r_work=0.1193 r_free=0.1600 | n_water=356 | time (s): 30.110 (total time: 30.900) Filter (q & B) r_work=0.1193 r_free=0.1600 | n_water=356 | time (s): 1.310 (total time: 32.210) Compute maps r_work=0.1193 r_free=0.1600 | n_water=356 | time (s): 0.720 (total time: 32.930) Filter (map) r_work=0.1255 r_free=0.1626 | n_water=261 | time (s): 2.150 (total time: 35.080) Find peaks r_work=0.1255 r_free=0.1626 | n_water=261 | time (s): 0.690 (total time: 35.770) Add new water r_work=0.1431 r_free=0.1771 | n_water=413 | time (s): 2.070 (total time: 37.840) Refine new water occ: r_work=0.1235 r_free=0.1568 adp: r_work=0.1227 r_free=0.1568 occ: r_work=0.1212 r_free=0.1549 adp: r_work=0.1202 r_free=0.1547 occ: r_work=0.1197 r_free=0.1534 adp: r_work=0.1188 r_free=0.1535 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1535 r_work=0.1188 r_free=0.1535 | n_water=413 | time (s): 32.750 (total time: 70.590) Filter (q & B) r_work=0.1191 r_free=0.1534 | n_water=399 | time (s): 2.360 (total time: 72.950) Filter (dist only) r_work=0.1191 r_free=0.1534 | n_water=399 | time (s): 31.650 (total time: 104.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.987279 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.175870 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1173 0.1512 0.0339 0.009 1.0 4.8 0.5 0.0 0 0.994 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.73 15.12 3.39 4.303 21.176 0.176 4.992 11.50 15.35 3.85 4.897 21.159 0.176 4.969 Individual atomic B min max mean iso aniso Overall: 6.38 104.43 20.61 4.86 1926 0 Protein: 6.38 104.43 16.85 4.85 1519 0 Water: 8.60 64.98 34.72 N/A 399 0 Other: 24.11 43.58 31.34 N/A 8 0 Chain A: 6.38 104.43 18.48 N/A 1730 0 Chain S: 19.40 64.98 39.41 N/A 196 0 Histogram: Values Number of atoms 6.38 - 16.18 1078 16.18 - 25.99 339 25.99 - 35.79 225 35.79 - 45.60 171 45.60 - 55.40 75 55.40 - 65.21 25 65.21 - 75.02 4 75.02 - 84.82 4 84.82 - 94.63 3 94.63 - 104.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1150 r_free=0.1535 r_work=0.1151 r_free=0.1537 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1537 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1526 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.25 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= 0.1149 r_free= 0.1526 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.967671 | | target function (ml) not normalized (work): 80645.177309 | | target function (ml) not normalized (free): 4184.892134 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1149 0.1526 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1651 0.1643 0.1848 n_refl.: 17041 remove outliers: r(all,work,free)=0.1651 0.1643 0.1848 n_refl.: 17041 overall B=-0.33 to atoms: r(all,work,free)=0.1630 0.1621 0.1838 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1167 0.1149 0.1526 n_refl.: 17041 remove outliers: r(all,work,free)=0.1166 0.1148 0.1526 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 0.3659 303.033 283.643 0.561 1.006 0.333 11.894-9.307 99.02 97 4 0.1786 487.726 479.831 0.913 1.007 0.328 9.237-7.194 100.00 213 7 0.1837 398.911 398.531 0.981 1.007 0.265 7.162-5.571 100.00 427 22 0.1587 299.383 294.354 0.941 1.007 0.251 5.546-4.326 100.00 867 58 0.0949 411.005 407.172 0.964 1.006 0.206 4.315-3.360 100.00 1859 96 0.0898 390.870 388.709 1.012 1.004 0.201 3.356-2.611 100.00 3867 181 0.1275 256.779 254.737 1.010 1.001 0.121 2.608-2.000 99.99 8818 434 0.1090 167.376 165.950 1.010 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1311 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1526 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1148 r_free=0.1526 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1526 | n_water=399 | time (s): 0.760 (total time: 0.760) Filter (dist) r_work=0.1148 r_free=0.1526 | n_water=399 | time (s): 34.320 (total time: 35.080) Filter (q & B) r_work=0.1148 r_free=0.1526 | n_water=399 | time (s): 0.980 (total time: 36.060) Compute maps r_work=0.1148 r_free=0.1526 | n_water=399 | time (s): 0.680 (total time: 36.740) Filter (map) r_work=0.1193 r_free=0.1551 | n_water=315 | time (s): 1.590 (total time: 38.330) Find peaks r_work=0.1193 r_free=0.1551 | n_water=315 | time (s): 0.460 (total time: 38.790) Add new water r_work=0.1332 r_free=0.1668 | n_water=453 | time (s): 1.810 (total time: 40.600) Refine new water occ: r_work=0.1177 r_free=0.1516 adp: r_work=0.1169 r_free=0.1517 occ: r_work=0.1155 r_free=0.1498 adp: r_work=0.1146 r_free=0.1496 occ: r_work=0.1141 r_free=0.1488 adp: r_work=0.1133 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1485 r_work=0.1133 r_free=0.1485 | n_water=453 | time (s): 34.380 (total time: 74.980) Filter (q & B) r_work=0.1138 r_free=0.1496 | n_water=442 | time (s): 1.770 (total time: 76.750) Filter (dist only) r_work=0.1138 r_free=0.1496 | n_water=441 | time (s): 34.930 (total time: 111.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.050470 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.195178 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 0.1128 0.1560 0.0432 0.010 1.0 4.8 0.5 0.0 0 1.025 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 15.60 4.32 4.586 20.939 0.195 4.960 11.16 15.70 4.54 4.715 21.033 0.195 4.951 Individual atomic B min max mean iso aniso Overall: 6.03 103.64 20.93 5.04 1968 0 Protein: 6.03 103.64 16.57 5.03 1519 0 Water: 8.71 63.84 35.86 N/A 441 0 Other: 18.78 39.10 26.17 N/A 8 0 Chain A: 6.03 103.64 18.14 N/A 1730 0 Chain S: 19.18 63.84 41.23 N/A 238 0 Histogram: Values Number of atoms 6.03 - 15.79 1063 15.79 - 25.55 356 25.55 - 35.31 218 35.31 - 45.08 187 45.08 - 54.84 97 54.84 - 64.60 31 64.60 - 74.36 8 74.36 - 84.12 3 84.12 - 93.88 2 93.88 - 103.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1116 r_free=0.1570 r_work=0.1116 r_free=0.1570 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1116 r_free = 0.1570 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1108 r_free = 0.1568 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1108 r_free= 0.1568 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.947472 | | target function (ml) not normalized (work): 80312.317168 | | target function (ml) not normalized (free): 4186.215936 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1108 0.1568 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1587 0.1576 0.1851 n_refl.: 17040 remove outliers: r(all,work,free)=0.1587 0.1576 0.1851 n_refl.: 17040 overall B=-0.27 to atoms: r(all,work,free)=0.1571 0.1559 0.1842 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1105 0.1559 n_refl.: 17040 remove outliers: r(all,work,free)=0.1127 0.1105 0.1559 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 0.3684 303.033 279.044 0.556 1.003 0.360 11.894-9.307 99.02 97 4 0.1722 487.726 482.383 0.912 1.004 0.340 9.237-7.194 100.00 213 7 0.1791 398.911 399.403 0.982 1.004 0.240 7.162-5.571 100.00 427 22 0.1534 299.383 293.744 0.935 1.004 0.215 5.546-4.326 100.00 867 58 0.0898 411.005 407.433 0.964 1.004 0.201 4.315-3.360 100.00 1859 96 0.0868 390.870 388.596 1.007 1.003 0.191 3.356-2.611 100.00 3867 181 0.1239 256.779 254.642 1.003 1.001 0.141 2.608-2.000 99.99 8818 434 0.1039 167.376 166.193 0.998 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9230 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1105 r_free=0.1559 After: r_work=0.1107 r_free=0.1558 ================================== NQH flips ================================== r_work=0.1107 r_free=0.1558 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1107 r_free=0.1558 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1107 r_free=0.1558 | n_water=441 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1110 r_free=0.1557 | n_water=440 | time (s): 34.170 (total time: 35.090) Filter (q & B) r_work=0.1110 r_free=0.1557 | n_water=437 | time (s): 2.050 (total time: 37.140) Compute maps r_work=0.1110 r_free=0.1557 | n_water=437 | time (s): 0.840 (total time: 37.980) Filter (map) r_work=0.1179 r_free=0.1565 | n_water=331 | time (s): 1.770 (total time: 39.750) Find peaks r_work=0.1179 r_free=0.1565 | n_water=331 | time (s): 0.470 (total time: 40.220) Add new water r_work=0.1309 r_free=0.1664 | n_water=471 | time (s): 1.650 (total time: 41.870) Refine new water occ: r_work=0.1150 r_free=0.1507 adp: r_work=0.1141 r_free=0.1509 occ: r_work=0.1128 r_free=0.1496 adp: r_work=0.1117 r_free=0.1497 occ: r_work=0.1112 r_free=0.1491 adp: r_work=0.1103 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1103 r_free=0.1490 r_work=0.1103 r_free=0.1490 | n_water=471 | time (s): 27.650 (total time: 69.520) Filter (q & B) r_work=0.1107 r_free=0.1505 | n_water=460 | time (s): 2.120 (total time: 71.640) Filter (dist only) r_work=0.1106 r_free=0.1505 | n_water=459 | time (s): 37.340 (total time: 108.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.850249 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.139604 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 0.1128 0.1510 0.0381 0.010 1.0 5.4 0.5 0.0 0 0.925 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 15.10 3.81 4.664 20.888 0.140 4.946 11.19 14.97 3.78 4.702 20.934 0.140 4.939 Individual atomic B min max mean iso aniso Overall: 5.93 102.05 21.00 4.95 1986 0 Protein: 5.93 102.05 16.29 4.95 1519 0 Water: 8.42 67.04 36.54 N/A 459 0 Other: 17.41 34.98 23.68 N/A 8 0 Chain A: 5.93 102.05 17.80 N/A 1728 0 Chain S: 19.10 67.04 42.45 N/A 258 0 Histogram: Values Number of atoms 5.93 - 15.54 1061 15.54 - 25.15 354 25.15 - 34.77 212 34.77 - 44.38 185 44.38 - 53.99 117 53.99 - 63.60 39 63.60 - 73.22 8 73.22 - 82.83 3 82.83 - 92.44 3 92.44 - 102.05 4 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1497 r_work=0.1119 r_free=0.1496 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1496 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1118 r_free = 0.1494 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1118 r_free= 0.1494 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.935855 | | target function (ml) not normalized (work): 80123.738839 | | target function (ml) not normalized (free): 4155.805227 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1126 0.1410 5.4628 5.6758| | 2: 3.63 - 2.88 1.00 2711 122 0.1120 0.1455 5.2289 5.3213| | 3: 2.88 - 2.52 1.00 2681 148 0.1367 0.1668 5.1341 5.19| | 4: 2.52 - 2.29 1.00 2661 139 0.0944 0.1465 4.6199 4.9218| | 5: 2.29 - 2.13 1.00 2678 122 0.0962 0.1425 4.5728 4.8502| | 6: 2.13 - 2.00 1.00 2692 117 0.1121 0.1723 4.5668 4.7879| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 8.99 1.00 0.96 6376.38| | 2: 3.63 - 2.88 2711 122 0.92 12.86 1.01 0.96 6376.38| | 3: 2.88 - 2.52 2681 148 0.87 18.99 0.99 0.96 6376.38| | 4: 2.52 - 2.29 2661 139 0.93 11.96 1.01 0.98 2068.30| | 5: 2.29 - 2.13 2678 122 0.92 13.91 1.00 0.98 2068.30| | 6: 2.13 - 2.00 2692 117 0.90 16.59 0.99 0.98 2068.30| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2068.30 max = 6376.38 mean = 4245.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.73 mean = 13.85| |phase err.(test): min = 0.00 max = 89.81 mean = 13.80| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1118 0.1494 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1576 0.1564 0.1823 n_refl.: 17040 remove outliers: r(all,work,free)=0.1576 0.1564 0.1823 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1562 0.1550 0.1815 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1120 0.1493 n_refl.: 17040 remove outliers: r(all,work,free)=0.1138 0.1120 0.1493 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 0.3661 303.033 279.602 0.540 1.001 0.330 11.894-9.307 99.02 97 4 0.1868 487.726 481.053 0.909 1.002 0.307 9.237-7.194 100.00 213 7 0.1767 398.911 399.008 0.987 1.003 0.230 7.162-5.571 100.00 427 22 0.1569 299.383 293.531 0.935 1.003 0.210 5.546-4.326 100.00 867 58 0.0923 411.005 407.769 0.968 1.003 0.190 4.315-3.360 100.00 1859 96 0.0894 390.870 388.654 1.007 1.002 0.191 3.356-2.611 100.00 3867 181 0.1256 256.779 254.470 1.001 1.001 0.131 2.608-2.000 99.99 8818 434 0.1042 167.376 166.015 0.991 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8289 ================= 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 : 0.2787 0.1786 0.080 5.131 8.8 119.3 19.9 258 0.000 1_bss: 0.1616 0.1660 0.080 5.131 8.5 118.9 19.5 258 0.000 1_settarget: 0.1616 0.1660 0.080 5.131 8.5 118.9 19.5 258 0.000 1_nqh: 0.1617 0.1662 0.080 5.131 8.5 118.9 19.5 258 0.003 1_weight: 0.1617 0.1662 0.080 5.131 8.5 118.9 19.5 258 0.003 1_xyzrec: 0.1349 0.1645 0.009 0.997 8.5 118.9 19.5 258 0.147 1_adp: 0.1278 0.1665 0.009 0.997 6.1 113.9 19.9 258 0.147 1_regHadp: 0.1281 0.1672 0.009 0.997 6.1 113.9 19.9 258 0.147 1_occ: 0.1277 0.1666 0.009 0.997 6.1 113.9 19.9 258 0.147 2_bss: 0.1274 0.1658 0.009 0.997 5.6 113.4 19.4 258 0.147 2_settarget: 0.1274 0.1658 0.009 0.997 5.6 113.4 19.4 258 0.147 2_updatecdl: 0.1274 0.1658 0.009 1.009 5.6 113.4 19.4 258 0.147 2_nqh: 0.1274 0.1658 0.009 1.009 5.6 113.4 19.4 258 0.147 2_sol: 0.1236 0.1569 0.009 1.009 5.6 112.2 20.5 357 n/a 2_weight: 0.1236 0.1569 0.009 1.009 5.6 112.2 20.5 357 n/a 2_xyzrec: 0.1211 0.1603 0.008 0.939 5.6 112.2 20.5 357 n/a 2_adp: 0.1196 0.1607 0.008 0.939 6.5 107.2 21.0 357 n/a 2_regHadp: 0.1197 0.1608 0.008 0.939 6.5 107.2 21.0 357 n/a 2_occ: 0.1193 0.1608 0.008 0.939 6.5 107.2 21.0 357 n/a 3_bss: 0.1190 0.1603 0.008 0.939 6.2 106.9 20.6 357 n/a 3_settarget: 0.1190 0.1603 0.008 0.939 6.2 106.9 20.6 357 n/a 3_updatecdl: 0.1190 0.1603 0.008 0.945 6.2 106.9 20.6 357 n/a 3_nqh: 0.1190 0.1603 0.008 0.945 6.2 106.9 20.6 357 n/a 3_sol: 0.1191 0.1534 0.008 0.945 6.2 106.9 20.6 399 n/a 3_weight: 0.1191 0.1534 0.008 0.945 6.2 106.9 20.6 399 n/a 3_xyzrec: 0.1173 0.1512 0.009 0.977 6.2 106.9 20.6 399 n/a 3_adp: 0.1150 0.1535 0.009 0.977 6.4 104.4 20.6 399 n/a 3_regHadp: 0.1151 0.1537 0.009 0.977 6.4 104.4 20.6 399 n/a 3_occ: 0.1149 0.1526 0.009 0.977 6.4 104.4 20.6 399 n/a 4_bss: 0.1148 0.1526 0.009 0.977 6.1 104.1 20.3 399 n/a 4_settarget: 0.1148 0.1526 0.009 0.977 6.1 104.1 20.3 399 n/a 4_updatecdl: 0.1148 0.1526 0.009 0.974 6.1 104.1 20.3 399 n/a 4_nqh: 0.1148 0.1526 0.009 0.974 6.1 104.1 20.3 399 n/a 4_sol: 0.1138 0.1496 0.009 0.974 6.1 104.1 20.8 441 n/a 4_weight: 0.1138 0.1496 0.009 0.974 6.1 104.1 20.8 441 n/a 4_xyzrec: 0.1128 0.1560 0.010 0.982 6.1 104.1 20.8 441 n/a 4_adp: 0.1116 0.1570 0.010 0.982 6.0 103.6 20.9 441 n/a 4_regHadp: 0.1116 0.1570 0.010 0.982 6.0 103.6 20.9 441 n/a 4_occ: 0.1108 0.1568 0.010 0.982 6.0 103.6 20.9 441 n/a 5_bss: 0.1105 0.1559 0.010 0.982 5.8 103.4 20.7 441 n/a 5_settarget: 0.1105 0.1559 0.010 0.982 5.8 103.4 20.7 441 n/a 5_updatecdl: 0.1105 0.1559 0.010 0.982 5.8 103.4 20.7 441 n/a 5_setrh: 0.1107 0.1558 0.010 0.982 5.8 103.4 20.7 441 n/a 5_nqh: 0.1107 0.1558 0.010 0.982 5.8 103.4 20.7 441 n/a 5_sol: 0.1106 0.1505 0.010 0.982 5.8 103.4 20.9 459 n/a 5_weight: 0.1106 0.1505 0.010 0.982 5.8 103.4 20.9 459 n/a 5_xyzrec: 0.1128 0.1510 0.010 1.045 5.8 103.4 20.9 459 n/a 5_adp: 0.1119 0.1497 0.010 1.045 5.9 102.1 21.0 459 n/a 5_regHadp: 0.1119 0.1496 0.010 1.045 5.9 102.1 21.0 459 n/a 5_occ: 0.1118 0.1494 0.010 1.045 5.9 102.1 21.0 459 n/a end: 0.1120 0.1493 0.010 1.045 5.7 101.8 20.8 459 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8954467_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8954467_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9600 Refinement macro-cycles (run) : 944.1300 Write final files (write_after_run_outputs) : 20.1900 Total : 967.2800 Total CPU time: 16.51 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:31 PST -0800 (1735494091.49 s) Start R-work = 0.1616, R-free = 0.1660 Final R-work = 0.1120, R-free = 0.1493 =============================================================================== Job complete usr+sys time: 1011.56 seconds wall clock time: 17 minutes 14.27 seconds (1034.27 seconds total)