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_5296401.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_5296401.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5296401.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 =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.02, per 1000 atoms: 0.60 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: 0.39 Conformation dependent library (CDL) restraints added in 133.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 473 0.90 - 1.15: 1153 1.15 - 1.40: 570 1.40 - 1.65: 892 1.65 - 1.90: 65 Bond restraints: 3153 Sorted by residual: bond pdb=" C PRO A 54 " pdb=" O PRO A 54 " ideal model delta sigma weight residual 1.233 0.986 0.247 1.21e-02 6.83e+03 4.15e+02 bond pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " ideal model delta sigma weight residual 1.326 1.538 -0.212 1.10e-02 8.26e+03 3.72e+02 bond pdb=" C ARG A 48 " pdb=" O ARG A 48 " ideal model delta sigma weight residual 1.233 0.985 0.249 1.30e-02 5.92e+03 3.66e+02 bond pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 1.461 1.678 -0.217 1.19e-02 7.06e+03 3.32e+02 bond pdb=" CA THR A 154 " pdb=" C THR A 154 " ideal model delta sigma weight residual 1.523 1.305 0.218 1.25e-02 6.40e+03 3.05e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.51: 3629 5.51 - 11.02: 1759 11.02 - 16.53: 351 16.53 - 22.04: 37 22.04 - 27.56: 1 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " pdb=" CG ASN A 144 " ideal model delta sigma weight residual 112.60 126.53 -13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" CA ALA A 103 " pdb=" C ALA A 103 " pdb=" O ALA A 103 " ideal model delta sigma weight residual 120.36 105.78 14.58 1.08e+00 8.57e-01 1.82e+02 angle pdb=" N ILE A 168 " pdb=" CA ILE A 168 " pdb=" C ILE A 168 " ideal model delta sigma weight residual 110.53 98.22 12.31 9.40e-01 1.13e+00 1.71e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 118.69 127.29 -8.60 6.70e-01 2.23e+00 1.65e+02 angle pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " pdb=" CG ASP A 49 " ideal model delta sigma weight residual 112.60 125.19 -12.59 1.00e+00 1.00e+00 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 1315 17.78 - 35.55: 111 35.55 - 53.33: 42 53.33 - 71.10: 12 71.10 - 88.88: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BASN A 97 " pdb=" N BASN A 97 " pdb=" CA BASN A 97 " pdb=" CB BASN A 97 " ideal model delta harmonic sigma weight residual -122.60 -140.64 18.04 0 2.50e+00 1.60e-01 5.21e+01 dihedral pdb=" N LEU A 10 " pdb=" C LEU A 10 " pdb=" CA LEU A 10 " pdb=" CB LEU A 10 " ideal model delta harmonic sigma weight residual 122.80 140.57 -17.77 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" C LEU A 10 " pdb=" N LEU A 10 " pdb=" CA LEU A 10 " pdb=" CB LEU A 10 " ideal model delta harmonic sigma weight residual -122.60 -140.07 17.47 0 2.50e+00 1.60e-01 4.88e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.210: 99 0.210 - 0.419: 84 0.419 - 0.629: 41 0.629 - 0.838: 16 0.838 - 1.047: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BASN A 97 " pdb=" N BASN A 97 " pdb=" C BASN A 97 " pdb=" CB BASN A 97 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA GLN A 180 " pdb=" N GLN A 180 " pdb=" C GLN A 180 " pdb=" CB GLN A 180 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" CA LEU A 10 " pdb=" N LEU A 10 " pdb=" C LEU A 10 " pdb=" CB LEU A 10 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.95e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.001 2.00e-02 2.50e+03 7.55e-02 1.71e+02 pdb=" CG TYR A 139 " -0.131 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.110 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.074 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.110 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.034 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.000 2.00e-02 2.50e+03 6.93e-02 1.44e+02 pdb=" CG BTYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.115 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.063 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.124 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.082 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.076 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " -0.072 2.00e-02 2.50e+03 7.08e-02 1.13e+02 pdb=" CG HIS A 138 " 0.062 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.108 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.096 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 800 2.29 - 2.87: 8017 2.87 - 3.45: 10551 3.45 - 4.02: 15288 4.02 - 4.60: 21979 Nonbonded interactions: 56635 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.715 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.735 2.270 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.776 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.824 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.840 2.450 ... (remaining 56630 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_5296401_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= 0.2794 r_free= 0.1842 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.399805 | | target function (ml) not normalized (work): 71466.030613 | | target function (ml) not normalized (free): 3266.026381 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3176 0.2108 7.4909 5.0209| | 2: 3.63 - 2.88 1.00 2711 122 0.2670 0.1895 4.3368 4.3546| | 3: 2.88 - 2.52 1.00 2682 148 0.2595 0.1660 4.1891 4.1985| | 4: 2.52 - 2.29 1.00 2661 139 0.2548 0.1510 3.5082 3.5354| | 5: 2.29 - 2.13 1.00 2678 122 0.2656 0.1517 3.3995 3.448| | 6: 2.13 - 2.00 1.00 2692 117 0.2746 0.1980 3.3126 3.4442| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.66 0.77 0.23 1313.55| | 2: 3.63 - 2.88 2711 122 0.83 23.95 1.32 0.23 1313.55| | 3: 2.88 - 2.52 2682 148 0.73 33.13 1.29 0.23 1313.55| | 4: 2.52 - 2.29 2661 139 0.94 10.93 1.30 0.26 128.43| | 5: 2.29 - 2.13 2678 122 0.92 13.03 1.32 0.26 128.43| | 6: 2.13 - 2.00 2692 117 0.90 15.86 1.33 0.26 128.43| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 128.43 max = 1313.55 mean = 727.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.89 mean = 19.10| |phase err.(test): min = 0.00 max = 89.89 mean = 19.14| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.257 1557 Z= 5.612 Angle : 5.206 18.205 2118 Z= 3.695 Chirality : 0.361 1.047 243 Planarity : 0.031 0.078 284 Dihedral : 13.883 88.878 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.62 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.81 % 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: -3.24 (0.44), residues: 224 helix: -2.80 (0.35), residues: 109 sheet: -0.82 (0.72), residues: 38 loop : -1.43 (0.59), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.026 ARG A 156 TYR 0.123 0.052 TYR A 141 PHE 0.067 0.030 PHE A 164 HIS 0.051 0.026 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2794 r_free= 0.1842 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.399805 | | target function (ml) not normalized (work): 71466.030613 | | target function (ml) not normalized (free): 3266.026381 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3427 percent. r_work = 0.2929 r_free = 0.2032 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2876 0.2929 0.2032 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2876 0.2929 0.2032 n_refl.: 17050 remove outliers: r(all,work,free)=0.2169 0.2179 0.2032 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2142 0.2152 0.2012 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1627 0.1624 0.1685 n_refl.: 17045 remove outliers: r(all,work,free)=0.1626 0.1623 0.1685 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 0.4047 394.898 359.410 0.642 1.011 0.387 11.894-9.307 99.02 97 4 0.1830 633.823 615.301 0.935 1.012 0.370 9.237-7.194 100.00 213 7 0.2148 518.403 509.763 0.959 1.011 0.371 7.162-5.571 100.00 427 22 0.2321 389.062 374.093 0.916 1.010 0.297 5.546-4.326 100.00 867 58 0.1388 534.120 527.638 0.963 1.008 0.233 4.315-3.360 100.00 1859 96 0.1286 507.953 503.316 1.017 1.005 0.201 3.356-2.611 100.00 3867 181 0.1677 333.696 329.145 1.016 1.000 0.081 2.608-2.000 99.99 8818 434 0.1666 217.513 213.452 1.028 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1623 r_free=0.1685 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1623 r_free=0.1685 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.718488 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.921732 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1352 0.1629 0.0276 0.009 1.0 1.0 0.5 0.0 0 11.859 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.29 2.76 3.013 18.454 0.922 0.023 12.80 16.50 3.70 3.594 18.676 0.922 0.021 Individual atomic B min max mean iso aniso Overall: 5.93 113.89 19.90 4.10 1785 0 Protein: 5.93 113.52 17.13 4.11 1519 0 Water: 8.57 113.89 36.05 N/A 258 0 Other: 21.38 36.87 25.91 N/A 8 0 Chain A: 5.93 113.89 19.90 N/A 1785 0 Histogram: Values Number of atoms 5.93 - 16.73 1076 16.73 - 27.53 347 27.53 - 38.32 189 38.32 - 49.12 90 49.12 - 59.91 56 59.91 - 70.71 12 70.71 - 81.51 7 81.51 - 92.30 4 92.30 - 103.10 1 103.10 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1280 r_free=0.1650 r_work=0.1283 r_free=0.1657 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1657 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 = 0.1650 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1280 r_free= 0.1650 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020181 | | target function (ls_wunit_k1) not normalized (work): 327.686309 | | target function (ls_wunit_k1) not normalized (free): 26.827119 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1298 0.1280 0.1650 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1911 0.1910 0.1978 n_refl.: 17044 remove outliers: r(all,work,free)=0.1911 0.1910 0.1978 n_refl.: 17044 overall B=-0.51 to atoms: r(all,work,free)=0.1874 0.1873 0.1959 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1645 n_refl.: 17044 remove outliers: r(all,work,free)=0.1294 0.1277 0.1645 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 96.88 88 5 0.3607 302.032 282.647 0.627 1.007 0.370 11.894-9.307 99.02 97 4 0.1657 488.944 477.819 0.919 1.007 0.366 9.237-7.194 100.00 213 7 0.1849 399.907 396.278 0.959 1.007 0.351 7.162-5.571 100.00 427 22 0.1869 300.131 294.522 0.930 1.006 0.301 5.546-4.326 100.00 867 58 0.1049 412.031 409.330 0.958 1.005 0.210 4.315-3.360 100.00 1859 96 0.0932 391.846 391.110 1.015 1.004 0.192 3.356-2.611 100.00 3867 181 0.1296 257.420 256.010 1.010 1.001 0.102 2.608-2.000 99.99 8818 434 0.1350 167.794 166.458 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1535 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1645 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1645 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1645 | n_water=258 | time (s): 0.890 (total time: 0.890) Filter (dist) r_work=0.1285 r_free=0.1632 | n_water=251 | time (s): 22.080 (total time: 22.970) Filter (q & B) r_work=0.1286 r_free=0.1633 | n_water=248 | time (s): 1.700 (total time: 24.670) Compute maps r_work=0.1286 r_free=0.1633 | n_water=248 | time (s): 0.850 (total time: 25.520) Filter (map) r_work=0.1325 r_free=0.1608 | n_water=207 | time (s): 2.240 (total time: 27.760) Find peaks r_work=0.1325 r_free=0.1608 | n_water=207 | time (s): 0.570 (total time: 28.330) Add new water r_work=0.1553 r_free=0.1864 | n_water=368 | time (s): 1.460 (total time: 29.790) Refine new water occ: r_work=0.1335 r_free=0.1614 adp: r_work=0.1276 r_free=0.1603 occ: r_work=0.1283 r_free=0.1585 adp: r_work=0.1249 r_free=0.1585 occ: r_work=0.1252 r_free=0.1581 adp: r_work=0.1240 r_free=0.1582 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1582 r_work=0.1240 r_free=0.1582 | n_water=368 | time (s): 16.080 (total time: 45.870) Filter (q & B) r_work=0.1241 r_free=0.1585 | n_water=361 | time (s): 1.730 (total time: 47.600) Filter (dist only) r_work=0.1241 r_free=0.1585 | n_water=360 | time (s): 30.740 (total time: 78.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.815065 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.006924 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 0.1214 0.1611 0.0398 0.008 0.9 2.6 0.5 0.0 0 12.408 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 16.11 3.98 4.178 20.797 1.007 0.018 11.96 16.29 4.33 4.242 21.076 1.007 0.018 Individual atomic B min max mean iso aniso Overall: 6.59 108.01 21.08 4.27 1887 0 Protein: 6.59 108.01 17.55 4.26 1519 0 Water: 8.36 68.44 35.70 N/A 360 0 Other: 24.04 42.53 32.24 N/A 8 0 Chain A: 6.59 108.01 19.23 N/A 1734 0 Chain S: 17.28 65.57 41.96 N/A 153 0 Histogram: Values Number of atoms 6.59 - 16.73 1041 16.73 - 26.87 372 26.87 - 37.01 215 37.01 - 47.16 157 47.16 - 57.30 69 57.30 - 67.44 22 67.44 - 77.58 4 77.58 - 87.73 5 87.73 - 97.87 0 97.87 - 108.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1629 r_work=0.1198 r_free=0.1631 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1631 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1635 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1197 r_free= 0.1635 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017169 | | target function (ls_wunit_k1) not normalized (work): 278.758768 | | target function (ls_wunit_k1) not normalized (free): 25.506530 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1197 0.1635 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1803 0.1799 0.1935 n_refl.: 17043 remove outliers: r(all,work,free)=0.1803 0.1799 0.1935 n_refl.: 17043 overall B=-0.42 to atoms: r(all,work,free)=0.1774 0.1770 0.1918 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1194 0.1626 n_refl.: 17043 remove outliers: r(all,work,free)=0.1213 0.1193 0.1626 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 0.3381 304.005 274.953 0.590 1.008 0.350 11.894-9.307 99.02 97 4 0.1531 488.944 485.562 0.917 1.008 0.344 9.237-7.194 100.00 213 7 0.1743 399.907 398.187 0.971 1.008 0.312 7.162-5.571 100.00 427 22 0.1575 300.131 296.931 0.934 1.007 0.295 5.546-4.326 100.00 867 58 0.0882 412.031 409.689 0.960 1.006 0.211 4.315-3.360 100.00 1859 96 0.0833 391.846 391.245 1.014 1.004 0.202 3.356-2.611 100.00 3867 181 0.1193 257.420 256.877 1.011 1.001 0.132 2.608-2.000 99.99 8818 434 0.1329 167.794 166.819 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1577 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1626 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=0.1194 r_free=0.1629 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1629 | n_water=360 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1194 r_free=0.1629 | n_water=359 | time (s): 30.340 (total time: 31.060) Filter (q & B) r_work=0.1194 r_free=0.1629 | n_water=358 | time (s): 1.740 (total time: 32.800) Compute maps r_work=0.1194 r_free=0.1629 | n_water=358 | time (s): 0.740 (total time: 33.540) Filter (map) r_work=0.1258 r_free=0.1633 | n_water=259 | time (s): 1.530 (total time: 35.070) Find peaks r_work=0.1258 r_free=0.1633 | n_water=259 | time (s): 0.430 (total time: 35.500) Add new water r_work=0.1463 r_free=0.1836 | n_water=404 | time (s): 1.390 (total time: 36.890) Refine new water occ: r_work=0.1257 r_free=0.1615 adp: r_work=0.1249 r_free=0.1618 occ: r_work=0.1230 r_free=0.1582 adp: r_work=0.1219 r_free=0.1584 occ: r_work=0.1211 r_free=0.1568 adp: r_work=0.1202 r_free=0.1567 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1567 r_work=0.1202 r_free=0.1567 | n_water=404 | time (s): 31.960 (total time: 68.850) Filter (q & B) r_work=0.1204 r_free=0.1569 | n_water=395 | time (s): 2.010 (total time: 70.860) Filter (dist only) r_work=0.1204 r_free=0.1569 | n_water=395 | time (s): 30.090 (total time: 100.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.907164 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160160 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 0.1184 0.1582 0.0398 0.009 1.0 4.2 0.5 0.0 0 0.954 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.84 15.82 3.98 4.316 21.179 0.160 5.013 11.64 15.95 4.30 4.824 21.071 0.160 4.993 Individual atomic B min max mean iso aniso Overall: 6.09 105.98 20.45 4.60 1922 0 Protein: 6.09 105.98 16.73 4.59 1519 0 Water: 8.27 61.09 34.52 N/A 395 0 Other: 25.74 44.07 33.33 N/A 8 0 Chain A: 6.09 105.98 18.38 N/A 1728 0 Chain S: 13.45 61.09 38.90 N/A 194 0 Histogram: Values Number of atoms 6.09 - 16.08 1076 16.08 - 26.07 342 26.07 - 36.06 231 36.06 - 46.05 172 46.05 - 56.03 62 56.03 - 66.02 27 66.02 - 76.01 5 76.01 - 86.00 3 86.00 - 95.99 2 95.99 - 105.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1164 r_free=0.1595 r_work=0.1165 r_free=0.1596 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1165 r_free = 0.1596 target_work(ml) = 4.993 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1156 r_free = 0.1587 target_work(ml) = 4.988 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1156 r_free= 0.1587 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.987844 | | target function (ml) not normalized (work): 80977.653240 | | target function (ml) not normalized (free): 4211.503629 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1176 0.1156 0.1587 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1665 0.1658 0.1857 n_refl.: 17042 remove outliers: r(all,work,free)=0.1665 0.1658 0.1857 n_refl.: 17042 overall B=-0.33 to atoms: r(all,work,free)=0.1643 0.1635 0.1847 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1174 0.1154 0.1588 n_refl.: 17042 remove outliers: r(all,work,free)=0.1173 0.1152 0.1588 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 0.3552 297.265 279.467 0.571 1.004 0.340 11.894-9.307 99.02 97 4 0.1816 488.944 480.739 0.915 1.005 0.340 9.237-7.194 100.00 213 7 0.1836 399.907 399.863 0.985 1.005 0.280 7.162-5.571 100.00 427 22 0.1667 300.131 294.788 0.942 1.004 0.241 5.546-4.326 100.00 867 58 0.0955 412.031 408.562 0.967 1.004 0.206 4.315-3.360 100.00 1859 96 0.0890 391.846 389.542 1.013 1.003 0.201 3.356-2.611 100.00 3867 181 0.1281 257.420 255.196 1.011 1.001 0.131 2.608-2.000 99.99 8818 434 0.1094 167.794 166.295 1.007 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1431 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1152 r_free=0.1588 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1152 r_free=0.1588 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1152 r_free=0.1588 | n_water=395 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1155 r_free=0.1589 | n_water=393 | time (s): 31.280 (total time: 31.940) Filter (q & B) r_work=0.1155 r_free=0.1589 | n_water=393 | time (s): 1.090 (total time: 33.030) Compute maps r_work=0.1155 r_free=0.1589 | n_water=393 | time (s): 0.720 (total time: 33.750) Filter (map) r_work=0.1209 r_free=0.1572 | n_water=304 | time (s): 1.630 (total time: 35.380) Find peaks r_work=0.1209 r_free=0.1572 | n_water=304 | time (s): 0.590 (total time: 35.970) Add new water r_work=0.1362 r_free=0.1751 | n_water=445 | time (s): 1.890 (total time: 37.860) Refine new water occ: r_work=0.1185 r_free=0.1576 adp: r_work=0.1179 r_free=0.1576 occ: r_work=0.1161 r_free=0.1556 adp: r_work=0.1153 r_free=0.1553 occ: r_work=0.1145 r_free=0.1542 adp: r_work=0.1138 r_free=0.1542 ADP+occupancy (water only), MIN, final r_work=0.1138 r_free=0.1542 r_work=0.1138 r_free=0.1542 | n_water=445 | time (s): 47.290 (total time: 85.150) Filter (q & B) r_work=0.1141 r_free=0.1548 | n_water=437 | time (s): 1.450 (total time: 86.600) Filter (dist only) r_work=0.1141 r_free=0.1548 | n_water=437 | time (s): 33.440 (total time: 120.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.953601 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.191034 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 0.1126 0.1579 0.0453 0.009 1.0 4.5 0.5 0.0 0 0.977 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.79 4.53 4.420 20.794 0.191 4.967 11.13 15.80 4.67 4.579 20.844 0.191 4.962 Individual atomic B min max mean iso aniso Overall: 5.59 105.30 20.74 4.90 1964 0 Protein: 5.59 105.30 16.37 4.89 1519 0 Water: 8.27 65.90 35.69 N/A 437 0 Other: 26.50 45.24 35.03 N/A 8 0 Chain A: 5.59 105.30 17.99 N/A 1727 0 Chain S: 14.62 65.90 40.79 N/A 237 0 Histogram: Values Number of atoms 5.59 - 15.56 1066 15.56 - 25.54 355 25.54 - 35.51 221 35.51 - 45.48 184 45.48 - 55.45 104 55.45 - 65.42 20 65.42 - 75.39 6 75.39 - 85.36 4 85.36 - 95.33 2 95.33 - 105.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1580 r_work=0.1114 r_free=0.1582 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1114 r_free = 0.1582 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1583 target_work(ml) = 4.958 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1583 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.957769 | | target function (ml) not normalized (work): 80479.459772 | | target function (ml) not normalized (free): 4198.339586 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1103 0.1583 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1591 0.1580 0.1852 n_refl.: 17040 remove outliers: r(all,work,free)=0.1591 0.1580 0.1852 n_refl.: 17040 overall B=-0.25 to atoms: r(all,work,free)=0.1576 0.1565 0.1845 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1100 0.1580 n_refl.: 17040 remove outliers: r(all,work,free)=0.1123 0.1100 0.1580 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 0.3617 297.265 275.597 0.548 1.004 0.330 11.894-9.307 99.02 97 4 0.1743 488.944 483.812 0.919 1.005 0.330 9.237-7.194 100.00 213 7 0.1697 399.907 400.221 0.986 1.005 0.270 7.162-5.571 100.00 427 22 0.1460 300.131 295.191 0.942 1.005 0.220 5.546-4.326 100.00 867 58 0.0904 412.031 408.360 0.962 1.004 0.201 4.315-3.360 100.00 1859 96 0.0849 391.846 388.964 1.004 1.003 0.191 3.356-2.611 100.00 3867 181 0.1241 257.420 254.955 1.000 1.001 0.141 2.608-2.000 99.99 8818 434 0.1047 167.794 166.562 0.994 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8577 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1580 After: r_work=0.1102 r_free=0.1578 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1578 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1578 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1578 | n_water=437 | time (s): 0.870 (total time: 0.870) Filter (dist) r_work=0.1102 r_free=0.1578 | n_water=437 | time (s): 33.980 (total time: 34.850) Filter (q & B) r_work=0.1102 r_free=0.1578 | n_water=437 | time (s): 1.360 (total time: 36.210) Compute maps r_work=0.1102 r_free=0.1578 | n_water=437 | time (s): 0.690 (total time: 36.900) Filter (map) r_work=0.1170 r_free=0.1557 | n_water=337 | time (s): 1.760 (total time: 38.660) Find peaks r_work=0.1170 r_free=0.1557 | n_water=337 | time (s): 0.440 (total time: 39.100) Add new water r_work=0.1297 r_free=0.1651 | n_water=471 | time (s): 1.630 (total time: 40.730) Refine new water occ: r_work=0.1145 r_free=0.1528 adp: r_work=0.1135 r_free=0.1531 occ: r_work=0.1124 r_free=0.1515 adp: r_work=0.1114 r_free=0.1517 occ: r_work=0.1109 r_free=0.1507 adp: r_work=0.1101 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1101 r_free=0.1510 r_work=0.1101 r_free=0.1510 | n_water=471 | time (s): 30.760 (total time: 71.490) Filter (q & B) r_work=0.1104 r_free=0.1514 | n_water=464 | time (s): 1.940 (total time: 73.430) Filter (dist only) r_work=0.1104 r_free=0.1514 | n_water=464 | time (s): 36.330 (total time: 109.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.949585 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.169348 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 0.1523 0.0402 0.010 1.0 8.0 0.5 0.0 0 0.975 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 15.23 4.02 4.572 20.750 0.169 4.952 11.10 15.04 3.94 4.638 20.823 0.169 4.941 Individual atomic B min max mean iso aniso Overall: 5.60 104.50 20.92 4.99 1991 0 Protein: 5.60 104.50 16.13 4.98 1519 0 Water: 7.85 66.72 36.41 N/A 464 0 Other: 25.98 43.97 33.63 N/A 8 0 Chain A: 5.60 104.50 17.71 N/A 1727 0 Chain S: 17.76 66.72 41.97 N/A 264 0 Histogram: Values Number of atoms 5.60 - 15.49 1068 15.49 - 25.38 356 25.38 - 35.27 212 35.27 - 45.16 190 45.16 - 55.05 119 55.05 - 64.94 30 64.94 - 74.83 7 74.83 - 84.72 4 84.72 - 94.61 3 94.61 - 104.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.1110 r_free=0.1504 r_work=0.1110 r_free=0.1504 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1110 r_free = 0.1504 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1105 r_free = 0.1499 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1105 r_free= 0.1499 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.935292 | | target function (ml) not normalized (work): 80114.601356 | | target function (ml) not normalized (free): 4162.246163 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1112 0.1330 5.4495 5.6112| | 2: 3.63 - 2.88 1.00 2711 122 0.1075 0.1555 5.204 5.3668| | 3: 2.88 - 2.52 1.00 2681 148 0.1347 0.1630 5.1109 5.1858| | 4: 2.52 - 2.29 1.00 2661 139 0.0941 0.1514 4.6385 4.9544| | 5: 2.29 - 2.13 1.00 2678 122 0.0983 0.1496 4.5933 4.9046| | 6: 2.13 - 2.00 1.00 2692 117 0.1138 0.1777 4.5865 4.793| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.74 1.00 0.96 6089.77| | 2: 3.63 - 2.88 2711 122 0.92 12.57 1.01 0.96 6089.77| | 3: 2.88 - 2.52 2681 148 0.88 18.68 0.99 0.96 6089.77| | 4: 2.52 - 2.29 2661 139 0.93 12.27 1.01 0.98 2175.36| | 5: 2.29 - 2.13 2678 122 0.91 14.31 1.00 0.98 2175.36| | 6: 2.13 - 2.00 2692 117 0.89 17.02 0.99 0.98 2175.36| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2175.36 max = 6089.77 mean = 4153.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.99 mean = 13.89| |phase err.(test): min = 0.00 max = 88.77 mean = 13.63| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1124 0.1105 0.1499 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1566 0.1555 0.1797 n_refl.: 17040 remove outliers: r(all,work,free)=0.1566 0.1555 0.1797 n_refl.: 17040 overall B=-0.21 to atoms: r(all,work,free)=0.1554 0.1543 0.1790 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1106 0.1501 n_refl.: 17040 remove outliers: r(all,work,free)=0.1126 0.1106 0.1501 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 0.3623 297.265 273.964 0.548 1.002 0.330 11.894-9.307 99.02 97 4 0.1766 488.944 482.200 0.921 1.002 0.303 9.237-7.194 100.00 213 7 0.1698 399.907 401.445 0.993 1.003 0.240 7.162-5.571 100.00 427 22 0.1525 300.131 294.016 0.938 1.002 0.215 5.546-4.326 100.00 867 58 0.0933 412.031 408.301 0.965 1.002 0.193 4.315-3.360 100.00 1859 96 0.0871 391.846 389.725 1.004 1.002 0.177 3.356-2.611 100.00 3867 181 0.1224 257.420 254.815 0.998 1.001 0.058 2.608-2.000 99.99 8818 434 0.1050 167.794 166.382 0.986 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7269 ================= 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 : 0.2794 0.1842 0.084 5.206 8.8 119.3 19.9 258 0.000 1_bss: 0.1623 0.1685 0.084 5.206 8.4 118.9 19.5 258 0.000 1_settarget: 0.1623 0.1685 0.084 5.206 8.4 118.9 19.5 258 0.000 1_nqh: 0.1623 0.1685 0.084 5.206 8.4 118.9 19.5 258 0.000 1_weight: 0.1623 0.1685 0.084 5.206 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1352 0.1629 0.009 0.976 8.4 118.9 19.5 258 0.142 1_adp: 0.1280 0.1650 0.009 0.976 5.9 113.9 19.9 258 0.142 1_regHadp: 0.1283 0.1657 0.009 0.976 5.9 113.9 19.9 258 0.142 1_occ: 0.1280 0.1650 0.009 0.976 5.9 113.9 19.9 258 0.142 2_bss: 0.1277 0.1645 0.009 0.976 5.4 113.4 19.4 258 0.142 2_settarget: 0.1277 0.1645 0.009 0.976 5.4 113.4 19.4 258 0.142 2_updatecdl: 0.1277 0.1645 0.009 0.994 5.4 113.4 19.4 258 0.142 2_nqh: 0.1277 0.1645 0.009 0.994 5.4 113.4 19.4 258 0.142 2_sol: 0.1241 0.1585 0.009 0.994 5.4 113.0 20.6 360 n/a 2_weight: 0.1241 0.1585 0.009 0.994 5.4 113.0 20.6 360 n/a 2_xyzrec: 0.1214 0.1611 0.008 0.932 5.4 113.0 20.6 360 n/a 2_adp: 0.1196 0.1629 0.008 0.932 6.6 108.0 21.1 360 n/a 2_regHadp: 0.1198 0.1631 0.008 0.932 6.6 108.0 21.1 360 n/a 2_occ: 0.1197 0.1635 0.008 0.932 6.6 108.0 21.1 360 n/a 3_bss: 0.1193 0.1626 0.008 0.932 6.2 107.6 20.7 360 n/a 3_settarget: 0.1193 0.1626 0.008 0.932 6.2 107.6 20.7 360 n/a 3_updatecdl: 0.1193 0.1626 0.008 0.933 6.2 107.6 20.7 360 n/a 3_nqh: 0.1194 0.1629 0.008 0.933 6.2 107.6 20.7 360 n/a 3_sol: 0.1204 0.1569 0.008 0.933 6.2 107.6 20.6 395 n/a 3_weight: 0.1204 0.1569 0.008 0.933 6.2 107.6 20.6 395 n/a 3_xyzrec: 0.1184 0.1582 0.009 0.956 6.2 107.6 20.6 395 n/a 3_adp: 0.1164 0.1595 0.009 0.956 6.1 106.0 20.5 395 n/a 3_regHadp: 0.1165 0.1596 0.009 0.956 6.1 106.0 20.5 395 n/a 3_occ: 0.1156 0.1587 0.009 0.956 6.1 106.0 20.5 395 n/a 4_bss: 0.1152 0.1588 0.009 0.956 5.8 105.6 20.1 395 n/a 4_settarget: 0.1152 0.1588 0.009 0.956 5.8 105.6 20.1 395 n/a 4_updatecdl: 0.1152 0.1588 0.009 0.955 5.8 105.6 20.1 395 n/a 4_nqh: 0.1152 0.1588 0.009 0.955 5.8 105.6 20.1 395 n/a 4_sol: 0.1141 0.1548 0.009 0.955 5.8 105.6 20.7 437 n/a 4_weight: 0.1141 0.1548 0.009 0.955 5.8 105.6 20.7 437 n/a 4_xyzrec: 0.1126 0.1579 0.009 0.969 5.8 105.6 20.7 437 n/a 4_adp: 0.1113 0.1580 0.009 0.969 5.6 105.3 20.7 437 n/a 4_regHadp: 0.1114 0.1582 0.009 0.969 5.6 105.3 20.7 437 n/a 4_occ: 0.1103 0.1583 0.009 0.969 5.6 105.3 20.7 437 n/a 5_bss: 0.1100 0.1580 0.009 0.969 5.3 105.1 20.5 437 n/a 5_settarget: 0.1100 0.1580 0.009 0.969 5.3 105.1 20.5 437 n/a 5_updatecdl: 0.1100 0.1580 0.009 0.970 5.3 105.1 20.5 437 n/a 5_setrh: 0.1102 0.1578 0.009 0.970 5.3 105.1 20.5 437 n/a 5_nqh: 0.1102 0.1578 0.009 0.970 5.3 105.1 20.5 437 n/a 5_sol: 0.1104 0.1514 0.009 0.970 5.3 105.1 20.8 464 n/a 5_weight: 0.1104 0.1514 0.009 0.970 5.3 105.1 20.8 464 n/a 5_xyzrec: 0.1121 0.1523 0.010 1.022 5.3 105.1 20.8 464 n/a 5_adp: 0.1110 0.1504 0.010 1.022 5.6 104.5 20.9 464 n/a 5_regHadp: 0.1110 0.1504 0.010 1.022 5.6 104.5 20.9 464 n/a 5_occ: 0.1105 0.1499 0.010 1.022 5.6 104.5 20.9 464 n/a end: 0.1106 0.1501 0.010 1.022 5.4 104.3 20.7 464 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5296401_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_5296401_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4200 Refinement macro-cycles (run) : 945.9100 Write final files (write_after_run_outputs) : 17.6200 Total : 966.9500 Total CPU time: 16.52 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:32 PST -0800 (1735494092.29 s) Start R-work = 0.1623, R-free = 0.1685 Final R-work = 0.1106, R-free = 0.1501 =============================================================================== Job complete usr+sys time: 1011.98 seconds wall clock time: 17 minutes 14.85 seconds (1034.85 seconds total)