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_1821005.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1821005.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1821005.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.56, per 1000 atoms: 0.46 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: 0.57 Conformation dependent library (CDL) restraints added in 216.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 527 0.91 - 1.17: 1108 1.17 - 1.42: 653 1.42 - 1.67: 828 1.67 - 1.93: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 1.354 1.582 -0.228 1.10e-02 8.26e+03 4.30e+02 bond pdb=" CA ALA A 178 " pdb=" C ALA A 178 " ideal model delta sigma weight residual 1.523 1.279 0.245 1.30e-02 5.92e+03 3.54e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.237 1.443 -0.206 1.17e-02 7.31e+03 3.11e+02 bond pdb=" CA ALA A 6 " pdb=" C ALA A 6 " ideal model delta sigma weight residual 1.522 1.313 0.209 1.22e-02 6.72e+03 2.93e+02 bond pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 1.459 1.252 0.207 1.25e-02 6.40e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 3031 4.44 - 8.87: 1883 8.87 - 13.30: 696 13.30 - 17.74: 146 17.74 - 22.17: 21 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 132.59 -13.39 9.00e-01 1.23e+00 2.21e+02 angle pdb=" CA ALA A 183 " pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 118.63 130.80 -12.17 9.20e-01 1.18e+00 1.75e+02 angle pdb=" O MET A 26 " pdb=" C MET A 26 " pdb=" N ARG A 27 " ideal model delta sigma weight residual 122.07 109.91 12.16 1.03e+00 9.43e-01 1.39e+02 angle pdb=" CG HIS A 115 " pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 107.20 118.86 -11.66 1.00e+00 1.00e+00 1.36e+02 angle pdb=" C PRO A 43 " pdb=" N VAL A 44 " pdb=" CA VAL A 44 " ideal model delta sigma weight residual 123.14 107.94 15.20 1.31e+00 5.83e-01 1.35e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 1294 16.71 - 33.42: 128 33.42 - 50.13: 45 50.13 - 66.84: 10 66.84 - 83.55: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ASN A 173 " pdb=" C ASN A 173 " pdb=" CA ASN A 173 " pdb=" CB ASN A 173 " ideal model delta harmonic sigma weight residual 122.80 144.47 -21.67 0 2.50e+00 1.60e-01 7.52e+01 dihedral pdb=" C THR A 160 " pdb=" N THR A 160 " pdb=" CA THR A 160 " pdb=" CB THR A 160 " ideal model delta harmonic sigma weight residual -122.00 -140.28 18.28 0 2.50e+00 1.60e-01 5.35e+01 dihedral pdb=" C ASN A 173 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " pdb=" CB ASN A 173 " ideal model delta harmonic sigma weight residual -122.60 -140.84 18.24 0 2.50e+00 1.60e-01 5.32e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.212: 95 0.212 - 0.416: 71 0.416 - 0.620: 51 0.620 - 0.823: 15 0.823 - 1.027: 11 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.56 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA THR A 160 " pdb=" N THR A 160 " pdb=" C THR A 160 " pdb=" CB THR A 160 " both_signs ideal model delta sigma weight residual False 2.53 1.51 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.54 1.01 2.00e-01 2.50e+01 2.54e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.048 2.00e-02 2.50e+03 8.37e-02 2.10e+02 pdb=" CG PHE A 119 " -0.178 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.060 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.125 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.067 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.075 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.037 2.00e-02 2.50e+03 5.39e-02 8.72e+01 pdb=" CG TYR A 139 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.116 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.093 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 57 " -0.046 2.00e-02 2.50e+03 8.74e-02 7.65e+01 pdb=" C SER A 57 " 0.151 2.00e-02 2.50e+03 pdb=" O SER A 57 " -0.060 2.00e-02 2.50e+03 pdb=" N LEU A 58 " -0.045 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1092 2.33 - 2.89: 8109 2.89 - 3.46: 10462 3.46 - 4.03: 15214 4.03 - 4.60: 21740 Nonbonded interactions: 56617 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.757 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.808 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.814 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.824 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.855 2.450 ... (remaining 56612 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_1821005_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= 0.1759 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.421600 | | target function (ml) not normalized (work): 71820.046316 | | target function (ml) not normalized (free): 3245.184820 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3187 0.2128 7.6702 5.0236| | 2: 3.63 - 2.88 1.00 2711 122 0.2647 0.1720 4.3167 4.3179| | 3: 2.88 - 2.52 1.00 2682 148 0.2582 0.1561 4.1706 4.1595| | 4: 2.52 - 2.29 1.00 2661 139 0.2584 0.1452 3.5029 3.54| | 5: 2.29 - 2.13 1.00 2678 122 0.2666 0.1411 3.4026 3.4392| | 6: 2.13 - 2.00 1.00 2692 117 0.2725 0.1719 3.2972 3.3537| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.20 0.77 0.23 1253.29| | 2: 3.63 - 2.88 2711 122 0.83 23.35 1.31 0.23 1253.29| | 3: 2.88 - 2.52 2682 148 0.74 32.22 1.29 0.23 1253.29| | 4: 2.52 - 2.29 2661 139 0.94 10.69 1.30 0.26 121.54| | 5: 2.29 - 2.13 2678 122 0.93 12.63 1.32 0.26 121.54| | 6: 2.13 - 2.00 2692 117 0.91 15.27 1.33 0.26 121.54| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 121.54 max = 1253.29 mean = 693.72| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.90 mean = 18.57| |phase err.(test): min = 0.00 max = 89.44 mean = 18.58| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.245 1557 Z= 5.298 Angle : 5.247 19.084 2118 Z= 3.703 Chirality : 0.399 1.027 243 Planarity : 0.032 0.090 284 Dihedral : 13.708 83.547 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.89 % Cbeta Deviations : 35.14 % 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: -2.52 (0.47), residues: 224 helix: -2.00 (0.41), residues: 107 sheet: -1.54 (0.67), residues: 38 loop : -0.83 (0.61), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.084 0.018 ARG A 27 TYR 0.085 0.034 TYR A 141 PHE 0.170 0.041 PHE A 119 HIS 0.028 0.017 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= 0.1759 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.421600 | | target function (ml) not normalized (work): 71820.046316 | | target function (ml) not normalized (free): 3245.184820 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3305 percent. r_work = 0.2927 r_free = 0.1917 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2870 0.2927 0.1917 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2870 0.2927 0.1917 n_refl.: 17050 remove outliers: r(all,work,free)=0.2162 0.2178 0.1917 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2134 0.2149 0.1903 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1613 0.1613 0.1614 n_refl.: 17045 remove outliers: r(all,work,free)=0.1611 0.1610 0.1614 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 0.3856 399.232 361.078 0.645 1.017 0.399 11.894-9.307 99.02 97 4 0.1879 634.075 616.690 0.926 1.017 0.380 9.237-7.194 100.00 213 7 0.2160 518.610 508.491 0.951 1.017 0.381 7.162-5.571 100.00 427 22 0.2262 389.217 376.328 0.920 1.015 0.290 5.546-4.326 100.00 867 58 0.1408 534.333 528.609 0.955 1.013 0.235 4.315-3.360 100.00 1859 96 0.1312 508.155 503.798 1.015 1.008 0.212 3.356-2.611 100.00 3867 181 0.1641 333.829 329.530 1.014 1.000 0.044 2.608-2.000 99.99 8818 434 0.1647 217.599 213.924 1.035 0.986 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4926 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1610 r_free=0.1614 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** A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1613 r_free=0.1621 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.229725 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.958360 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 0.1350 0.1648 0.0299 0.009 1.0 1.3 0.5 0.0 0 11.615 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.48 2.99 3.013 18.440 0.958 0.022 12.73 16.67 3.94 3.661 18.747 0.958 0.020 Individual atomic B min max mean iso aniso Overall: 6.18 113.88 20.05 4.10 1785 0 Protein: 6.18 112.82 17.29 4.10 1519 0 Water: 8.83 113.88 36.10 N/A 258 0 Other: 22.18 36.93 26.69 N/A 8 0 Chain A: 6.18 113.88 20.05 N/A 1785 0 Histogram: Values Number of atoms 6.18 - 16.95 1084 16.95 - 27.72 338 27.72 - 38.49 189 38.49 - 49.26 100 49.26 - 60.03 45 60.03 - 70.80 15 70.80 - 81.57 6 81.57 - 92.34 4 92.34 - 103.11 1 103.11 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1273 r_free=0.1667 r_work=0.1277 r_free=0.1674 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1277 r_free = 0.1674 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 = 0.1272 r_free = 0.1667 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= 0.1272 r_free= 0.1667 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019756 | | target function (ls_wunit_k1) not normalized (work): 320.759555 | | target function (ls_wunit_k1) not normalized (free): 27.560819 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1272 0.1667 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1915 0.1913 0.1999 n_refl.: 17043 remove outliers: r(all,work,free)=0.1915 0.1913 0.1999 n_refl.: 17043 overall B=-0.40 to atoms: r(all,work,free)=0.1885 0.1883 0.1982 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1290 0.1272 0.1655 n_refl.: 17043 remove outliers: r(all,work,free)=0.1289 0.1270 0.1655 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 0.3417 306.047 280.538 0.634 1.002 0.370 11.894-9.307 99.02 97 4 0.1677 486.966 476.469 0.925 1.002 0.367 9.237-7.194 100.00 213 7 0.1800 398.289 395.957 0.965 1.001 0.351 7.162-5.571 100.00 427 22 0.1828 298.917 294.007 0.939 1.000 0.264 5.546-4.326 100.00 867 58 0.1044 410.365 407.625 0.965 0.997 0.210 4.315-3.360 100.00 1859 96 0.0925 390.261 389.796 1.030 0.992 0.191 3.356-2.611 100.00 3867 181 0.1292 256.379 255.168 1.032 0.985 0.091 2.608-2.000 99.99 8818 434 0.1350 167.115 165.721 1.047 0.971 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4278 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1270 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1272 r_free=0.1658 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1658 | n_water=258 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1280 r_free=0.1643 | n_water=252 | time (s): 20.560 (total time: 21.360) Filter (q & B) r_work=0.1280 r_free=0.1643 | n_water=250 | time (s): 2.170 (total time: 23.530) Compute maps r_work=0.1280 r_free=0.1643 | n_water=250 | time (s): 0.710 (total time: 24.240) Filter (map) r_work=0.1322 r_free=0.1637 | n_water=208 | time (s): 1.640 (total time: 25.880) Find peaks r_work=0.1322 r_free=0.1637 | n_water=208 | time (s): 0.430 (total time: 26.310) Add new water r_work=0.1548 r_free=0.1890 | n_water=369 | time (s): 1.510 (total time: 27.820) Refine new water occ: r_work=0.1335 r_free=0.1606 adp: r_work=0.1273 r_free=0.1605 occ: r_work=0.1280 r_free=0.1569 adp: r_work=0.1245 r_free=0.1577 occ: r_work=0.1247 r_free=0.1564 adp: r_work=0.1235 r_free=0.1567 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1567 r_work=0.1235 r_free=0.1567 | n_water=369 | time (s): 24.320 (total time: 52.140) Filter (q & B) r_work=0.1237 r_free=0.1571 | n_water=361 | time (s): 1.630 (total time: 53.770) Filter (dist only) r_work=0.1237 r_free=0.1575 | n_water=360 | time (s): 26.220 (total time: 79.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.975270 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.939962 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 0.1208 0.1581 0.0373 0.008 0.9 2.2 0.5 0.0 0 11.988 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 15.81 3.73 4.191 21.128 0.940 0.018 11.94 16.02 4.08 4.187 21.404 0.940 0.018 Individual atomic B min max mean iso aniso Overall: 6.35 107.42 21.40 4.24 1887 0 Protein: 6.35 107.42 17.83 4.23 1519 0 Water: 9.02 65.99 36.20 N/A 360 0 Other: 24.78 43.95 34.24 N/A 8 0 Chain A: 6.35 107.42 19.52 N/A 1735 0 Chain S: 17.10 65.99 42.88 N/A 152 0 Histogram: Values Number of atoms 6.35 - 16.46 1001 16.46 - 26.57 387 26.57 - 36.67 231 36.67 - 46.78 164 46.78 - 56.89 69 56.89 - 66.99 25 66.99 - 77.10 3 77.10 - 87.21 4 87.21 - 97.31 1 97.31 - 107.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1602 r_work=0.1195 r_free=0.1603 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1603 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1601 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 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= 0.1192 r_free= 0.1601 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016949 | | target function (ls_wunit_k1) not normalized (work): 275.151461 | | target function (ls_wunit_k1) not normalized (free): 24.656819 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1192 0.1601 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1750 0.1742 0.1948 n_refl.: 17041 remove outliers: r(all,work,free)=0.1750 0.1742 0.1948 n_refl.: 17041 overall B=-0.39 to atoms: r(all,work,free)=0.1725 0.1716 0.1930 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1187 0.1591 n_refl.: 17041 remove outliers: r(all,work,free)=0.1207 0.1187 0.1591 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 0.3332 306.047 284.017 0.592 1.005 0.340 11.894-9.307 99.02 97 4 0.1512 486.966 483.248 0.914 1.006 0.340 9.237-7.194 100.00 213 7 0.1640 398.289 399.636 0.972 1.005 0.289 7.162-5.571 100.00 427 22 0.1566 298.917 294.850 0.936 1.005 0.261 5.546-4.326 100.00 867 58 0.0893 410.365 407.703 0.959 1.004 0.216 4.315-3.360 100.00 1859 96 0.0823 390.261 389.469 1.017 1.003 0.211 3.356-2.611 100.00 3867 181 0.1188 256.379 255.620 1.013 1.001 0.101 2.608-2.000 99.99 8818 434 0.1329 167.115 166.100 1.020 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4022 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1591 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1591 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1591 | n_water=360 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1188 r_free=0.1595 | n_water=359 | time (s): 29.970 (total time: 30.590) Filter (q & B) r_work=0.1188 r_free=0.1595 | n_water=359 | time (s): 1.020 (total time: 31.610) Compute maps r_work=0.1188 r_free=0.1595 | n_water=359 | time (s): 0.730 (total time: 32.340) Filter (map) r_work=0.1257 r_free=0.1618 | n_water=261 | time (s): 2.330 (total time: 34.670) Find peaks r_work=0.1257 r_free=0.1618 | n_water=261 | time (s): 0.660 (total time: 35.330) Add new water r_work=0.1436 r_free=0.1749 | n_water=406 | time (s): 1.620 (total time: 36.950) Refine new water occ: r_work=0.1244 r_free=0.1556 adp: r_work=0.1234 r_free=0.1557 occ: r_work=0.1219 r_free=0.1536 adp: r_work=0.1207 r_free=0.1536 occ: r_work=0.1200 r_free=0.1528 adp: r_work=0.1190 r_free=0.1527 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1527 r_work=0.1190 r_free=0.1527 | n_water=406 | time (s): 35.790 (total time: 72.740) Filter (q & B) r_work=0.1192 r_free=0.1530 | n_water=400 | time (s): 1.550 (total time: 74.290) Filter (dist only) r_work=0.1192 r_free=0.1530 | n_water=400 | time (s): 30.940 (total time: 105.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.791387 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.137460 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 0.1178 0.1521 0.0343 0.009 1.0 5.4 0.5 0.0 0 0.896 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.78 15.21 3.43 4.328 21.561 0.137 4.987 11.58 15.51 3.93 4.863 21.487 0.137 4.969 Individual atomic B min max mean iso aniso Overall: 6.49 103.61 20.88 4.69 1927 0 Protein: 6.49 103.61 17.09 4.68 1519 0 Water: 8.88 63.51 35.05 N/A 400 0 Other: 26.07 43.76 33.37 N/A 8 0 Chain A: 6.49 103.61 18.75 N/A 1730 0 Chain S: 18.95 63.51 39.59 N/A 197 0 Histogram: Values Number of atoms 6.49 - 16.20 1048 16.20 - 25.91 357 25.91 - 35.62 225 35.62 - 45.34 175 45.34 - 55.05 83 55.05 - 64.76 26 64.76 - 74.47 4 74.47 - 84.18 4 84.18 - 93.90 3 93.90 - 103.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1551 r_work=0.1158 r_free=0.1553 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1553 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1542 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.17 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= 0.1151 r_free= 0.1542 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.962337 | | target function (ml) not normalized (work): 80558.581668 | | target function (ml) not normalized (free): 4173.184967 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1170 0.1151 0.1542 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1674 0.1667 0.1852 n_refl.: 17041 remove outliers: r(all,work,free)=0.1674 0.1667 0.1852 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1648 0.1640 0.1839 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1170 0.1150 0.1545 n_refl.: 17041 remove outliers: r(all,work,free)=0.1169 0.1150 0.1545 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 0.3503 302.561 280.008 0.574 1.006 0.347 11.894-9.307 99.02 97 4 0.1727 486.966 478.955 0.907 1.006 0.345 9.237-7.194 100.00 213 7 0.1785 398.289 398.596 0.982 1.006 0.260 7.162-5.571 100.00 427 22 0.1602 298.917 293.914 0.942 1.006 0.232 5.546-4.326 100.00 867 58 0.0950 410.365 406.862 0.962 1.005 0.205 4.315-3.360 100.00 1859 96 0.0892 390.261 387.930 1.011 1.003 0.188 3.356-2.611 100.00 3867 181 0.1278 256.379 254.168 1.013 1.000 0.131 2.608-2.000 99.99 8818 434 0.1103 167.115 165.700 1.018 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3492 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1150 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1150 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1150 r_free=0.1545 | n_water=400 | time (s): 0.820 (total time: 0.820) Filter (dist) r_work=0.1150 r_free=0.1545 | n_water=400 | time (s): 29.820 (total time: 30.640) Filter (q & B) r_work=0.1150 r_free=0.1545 | n_water=399 | time (s): 2.050 (total time: 32.690) Compute maps r_work=0.1150 r_free=0.1545 | n_water=399 | time (s): 0.840 (total time: 33.530) Filter (map) r_work=0.1198 r_free=0.1584 | n_water=313 | time (s): 2.150 (total time: 35.680) Find peaks r_work=0.1198 r_free=0.1584 | n_water=313 | time (s): 0.510 (total time: 36.190) Add new water r_work=0.1337 r_free=0.1659 | n_water=454 | time (s): 1.510 (total time: 37.700) Refine new water occ: r_work=0.1173 r_free=0.1523 adp: r_work=0.1164 r_free=0.1523 occ: r_work=0.1152 r_free=0.1509 adp: r_work=0.1141 r_free=0.1507 occ: r_work=0.1137 r_free=0.1497 adp: r_work=0.1128 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1498 r_work=0.1128 r_free=0.1498 | n_water=454 | time (s): 37.040 (total time: 74.740) Filter (q & B) r_work=0.1131 r_free=0.1496 | n_water=448 | time (s): 1.770 (total time: 76.510) Filter (dist only) r_work=0.1133 r_free=0.1493 | n_water=447 | time (s): 37.510 (total time: 114.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.976755 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.134123 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 0.1116 0.1546 0.0430 0.010 1.0 4.2 0.5 0.0 0 0.988 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.46 4.30 4.510 21.216 0.134 4.954 11.06 15.40 4.34 4.707 21.210 0.134 4.945 Individual atomic B min max mean iso aniso Overall: 6.08 99.27 21.05 4.74 1974 0 Protein: 6.08 99.27 16.61 4.74 1519 0 Water: 8.72 63.82 35.98 N/A 447 0 Other: 24.38 39.86 30.90 N/A 8 0 Chain A: 6.08 99.27 18.19 N/A 1728 0 Chain S: 16.10 63.82 41.16 N/A 246 0 Histogram: Values Number of atoms 6.08 - 15.40 1019 15.40 - 24.72 375 24.72 - 34.04 215 34.04 - 43.36 196 43.36 - 52.68 108 52.68 - 62.00 40 62.00 - 71.32 10 71.32 - 80.63 4 80.63 - 89.95 3 89.95 - 99.27 4 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1540 r_work=0.1106 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1541 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1542 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.23 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= 0.1100 r_free= 0.1542 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.941365 | | target function (ml) not normalized (work): 80213.173783 | | target function (ml) not normalized (free): 4173.109216 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1100 0.1542 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1579 0.1567 0.1838 n_refl.: 17040 remove outliers: r(all,work,free)=0.1579 0.1567 0.1838 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1560 0.1548 0.1828 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1098 0.1538 n_refl.: 17040 remove outliers: r(all,work,free)=0.1120 0.1098 0.1538 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 0.3597 302.561 275.977 0.560 1.004 0.350 11.894-9.307 99.02 97 4 0.1746 486.966 479.952 0.908 1.004 0.330 9.237-7.194 100.00 213 7 0.1797 398.289 399.426 0.986 1.004 0.235 7.162-5.571 100.00 427 22 0.1549 298.917 292.784 0.940 1.004 0.220 5.546-4.326 100.00 867 58 0.0912 410.365 407.050 0.964 1.003 0.190 4.315-3.360 100.00 1859 96 0.0855 390.261 388.178 1.008 1.002 0.181 3.356-2.611 100.00 3867 181 0.1213 256.379 254.330 1.007 1.001 0.121 2.608-2.000 99.99 8818 434 0.1042 167.115 165.920 1.004 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0489 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1098 r_free=0.1538 After: r_work=0.1101 r_free=0.1537 ================================== NQH flips ================================== r_work=0.1101 r_free=0.1537 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1101 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1101 r_free=0.1537 | n_water=447 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1101 r_free=0.1537 | n_water=447 | time (s): 37.130 (total time: 37.770) Filter (q & B) r_work=0.1101 r_free=0.1537 | n_water=447 | time (s): 0.930 (total time: 38.700) Compute maps r_work=0.1101 r_free=0.1537 | n_water=447 | time (s): 0.790 (total time: 39.490) Filter (map) r_work=0.1174 r_free=0.1548 | n_water=339 | time (s): 2.410 (total time: 41.900) Find peaks r_work=0.1174 r_free=0.1548 | n_water=339 | time (s): 0.430 (total time: 42.330) Add new water r_work=0.1279 r_free=0.1661 | n_water=473 | time (s): 1.860 (total time: 44.190) Refine new water occ: r_work=0.1135 r_free=0.1505 adp: r_work=0.1128 r_free=0.1508 occ: r_work=0.1117 r_free=0.1489 adp: r_work=0.1109 r_free=0.1492 occ: r_work=0.1104 r_free=0.1479 adp: r_work=0.1097 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1097 r_free=0.1482 r_work=0.1097 r_free=0.1482 | n_water=473 | time (s): 31.190 (total time: 75.380) Filter (q & B) r_work=0.1101 r_free=0.1486 | n_water=465 | time (s): 1.610 (total time: 76.990) Filter (dist only) r_work=0.1101 r_free=0.1488 | n_water=464 | time (s): 38.090 (total time: 115.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.856985 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.165544 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 0.1118 0.1519 0.0401 0.010 1.1 5.1 0.5 0.0 0 0.928 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 15.19 4.01 4.485 20.855 0.166 4.940 11.08 15.12 4.04 4.587 20.919 0.166 4.932 Individual atomic B min max mean iso aniso Overall: 5.63 99.91 20.99 5.03 1991 0 Protein: 5.63 99.91 16.34 5.02 1519 0 Water: 8.64 64.64 36.04 N/A 464 0 Other: 22.10 40.99 30.84 N/A 8 0 Chain A: 5.63 99.91 17.90 N/A 1728 0 Chain S: 17.24 64.64 41.26 N/A 263 0 Histogram: Values Number of atoms 5.63 - 15.05 1026 15.05 - 24.48 366 24.48 - 33.91 226 33.91 - 43.34 195 43.34 - 52.77 116 52.77 - 62.20 38 62.20 - 71.63 14 71.63 - 81.05 2 81.05 - 90.48 4 90.48 - 99.91 4 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1512 r_work=0.1108 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1512 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1503 target_work(ml) = 4.926 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1101 r_free= 0.1503 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.925972 | | target function (ml) not normalized (work): 79963.304307 | | target function (ml) not normalized (free): 4152.760360 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1114 0.1391 5.455 5.6371| | 2: 3.63 - 2.88 1.00 2711 122 0.1073 0.1466 5.2079 5.3255| | 3: 2.88 - 2.52 1.00 2681 148 0.1343 0.1696 5.1195 5.2079| | 4: 2.52 - 2.29 1.00 2661 139 0.0928 0.1485 4.6132 4.9104| | 5: 2.29 - 2.13 1.00 2678 122 0.0967 0.1501 4.5672 4.8875| | 6: 2.13 - 2.00 1.00 2692 117 0.1136 0.1702 4.5632 4.7621| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.85 1.00 0.96 6221.07| | 2: 3.63 - 2.88 2711 122 0.93 12.56 1.01 0.96 6221.07| | 3: 2.88 - 2.52 2681 148 0.88 18.78 0.99 0.96 6221.07| | 4: 2.52 - 2.29 2661 139 0.93 11.91 1.01 0.97 2035.97| | 5: 2.29 - 2.13 2678 122 0.92 13.90 1.00 0.97 2035.97| | 6: 2.13 - 2.00 2692 117 0.90 16.55 0.99 0.97 2035.97| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2035.97 max = 6221.07 mean = 4150.56| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.72| |phase err.(test): min = 0.00 max = 86.70 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1101 0.1503 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1570 0.1559 0.1805 n_refl.: 17040 remove outliers: r(all,work,free)=0.1570 0.1559 0.1805 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1556 0.1545 0.1798 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1102 0.1505 n_refl.: 17040 remove outliers: r(all,work,free)=0.1122 0.1102 0.1505 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 0.3507 302.561 281.776 0.559 1.006 0.340 11.894-9.307 99.02 97 4 0.1697 486.966 480.794 0.908 1.006 0.307 9.237-7.194 100.00 213 7 0.1801 398.289 399.138 0.985 1.006 0.225 7.162-5.571 100.00 427 22 0.1588 298.917 292.716 0.934 1.005 0.220 5.546-4.326 100.00 867 58 0.0912 410.365 407.185 0.962 1.005 0.198 4.315-3.360 100.00 1859 96 0.0873 390.261 388.319 1.002 1.003 0.181 3.356-2.611 100.00 3867 181 0.1215 256.379 254.507 1.001 1.000 0.101 2.608-2.000 99.99 8818 434 0.1042 167.115 165.742 0.993 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7932 ================= 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 0.1759 0.081 5.247 8.8 119.3 19.9 258 0.000 1_bss: 0.1610 0.1614 0.081 5.247 8.4 118.9 19.5 258 0.000 1_settarget: 0.1610 0.1614 0.081 5.247 8.4 118.9 19.5 258 0.000 1_nqh: 0.1613 0.1621 0.081 5.247 8.4 118.9 19.5 258 0.003 1_weight: 0.1613 0.1621 0.081 5.247 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1350 0.1648 0.009 0.978 8.4 118.9 19.5 258 0.152 1_adp: 0.1273 0.1667 0.009 0.978 6.2 113.9 20.0 258 0.152 1_regHadp: 0.1277 0.1674 0.009 0.978 6.2 113.9 20.0 258 0.152 1_occ: 0.1272 0.1667 0.009 0.978 6.2 113.9 20.0 258 0.152 2_bss: 0.1270 0.1655 0.009 0.978 5.8 113.5 19.6 258 0.152 2_settarget: 0.1270 0.1655 0.009 0.978 5.8 113.5 19.6 258 0.152 2_updatecdl: 0.1270 0.1655 0.009 0.987 5.8 113.5 19.6 258 0.152 2_nqh: 0.1272 0.1658 0.009 0.987 5.8 113.5 19.6 258 0.149 2_sol: 0.1237 0.1575 0.009 0.987 5.8 112.4 20.9 360 n/a 2_weight: 0.1237 0.1575 0.009 0.987 5.8 112.4 20.9 360 n/a 2_xyzrec: 0.1208 0.1581 0.008 0.925 5.8 112.4 20.9 360 n/a 2_adp: 0.1194 0.1602 0.008 0.925 6.4 107.4 21.4 360 n/a 2_regHadp: 0.1195 0.1603 0.008 0.925 6.4 107.4 21.4 360 n/a 2_occ: 0.1192 0.1601 0.008 0.925 6.4 107.4 21.4 360 n/a 3_bss: 0.1187 0.1591 0.008 0.925 6.0 107.0 21.0 360 n/a 3_settarget: 0.1187 0.1591 0.008 0.925 6.0 107.0 21.0 360 n/a 3_updatecdl: 0.1187 0.1591 0.008 0.931 6.0 107.0 21.0 360 n/a 3_nqh: 0.1187 0.1591 0.008 0.931 6.0 107.0 21.0 360 n/a 3_sol: 0.1192 0.1530 0.008 0.931 6.0 107.0 21.0 400 n/a 3_weight: 0.1192 0.1530 0.008 0.931 6.0 107.0 21.0 400 n/a 3_xyzrec: 0.1178 0.1521 0.009 0.965 6.0 107.0 21.0 400 n/a 3_adp: 0.1158 0.1551 0.009 0.965 6.5 103.6 20.9 400 n/a 3_regHadp: 0.1158 0.1553 0.009 0.965 6.5 103.6 20.9 400 n/a 3_occ: 0.1151 0.1542 0.009 0.965 6.5 103.6 20.9 400 n/a 4_bss: 0.1150 0.1545 0.009 0.965 6.1 103.2 20.5 400 n/a 4_settarget: 0.1150 0.1545 0.009 0.965 6.1 103.2 20.5 400 n/a 4_updatecdl: 0.1150 0.1545 0.009 0.963 6.1 103.2 20.5 400 n/a 4_nqh: 0.1150 0.1545 0.009 0.963 6.1 103.2 20.5 400 n/a 4_sol: 0.1133 0.1493 0.009 0.963 6.1 103.2 21.1 447 n/a 4_weight: 0.1133 0.1493 0.009 0.963 6.1 103.2 21.1 447 n/a 4_xyzrec: 0.1116 0.1546 0.010 0.987 6.1 103.2 21.1 447 n/a 4_adp: 0.1106 0.1540 0.010 0.987 6.1 99.3 21.1 447 n/a 4_regHadp: 0.1106 0.1541 0.010 0.987 6.1 99.3 21.1 447 n/a 4_occ: 0.1100 0.1542 0.010 0.987 6.1 99.3 21.1 447 n/a 5_bss: 0.1098 0.1538 0.010 0.987 5.8 99.0 20.7 447 n/a 5_settarget: 0.1098 0.1538 0.010 0.987 5.8 99.0 20.7 447 n/a 5_updatecdl: 0.1098 0.1538 0.010 0.987 5.8 99.0 20.7 447 n/a 5_setrh: 0.1101 0.1537 0.010 0.987 5.8 99.0 20.7 447 n/a 5_nqh: 0.1101 0.1537 0.010 0.987 5.8 99.0 20.7 447 n/a 5_sol: 0.1101 0.1488 0.010 0.987 5.8 99.0 20.9 464 n/a 5_weight: 0.1101 0.1488 0.010 0.987 5.8 99.0 20.9 464 n/a 5_xyzrec: 0.1118 0.1519 0.010 1.074 5.8 99.0 20.9 464 n/a 5_adp: 0.1108 0.1512 0.010 1.074 5.6 99.9 21.0 464 n/a 5_regHadp: 0.1108 0.1512 0.010 1.074 5.6 99.9 21.0 464 n/a 5_occ: 0.1101 0.1503 0.010 1.074 5.6 99.9 21.0 464 n/a end: 0.1102 0.1505 0.010 1.074 5.4 99.7 20.8 464 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1821005_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1821005_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.2800 Refinement macro-cycles (run) : 951.6100 Write final files (write_after_run_outputs) : 17.6800 Total : 973.5700 Total CPU time: 16.60 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:37 PST -0800 (1735494097.14 s) Start R-work = 0.1610, R-free = 0.1614 Final R-work = 0.1102, R-free = 0.1505 =============================================================================== Job complete usr+sys time: 1016.97 seconds wall clock time: 17 minutes 19.85 seconds (1039.85 seconds total)