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_3850167.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3850167.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3850167.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" 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" } 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: 1.08, per 1000 atoms: 0.32 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: 0.35 Conformation dependent library (CDL) restraints added in 103.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 601 0.92 - 1.19: 1081 1.19 - 1.46: 774 1.46 - 1.73: 684 1.73 - 2.00: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.486 -0.147 7.50e-03 1.78e+04 3.83e+02 bond pdb=" N GLU A 143 " pdb=" CA GLU A 143 " ideal model delta sigma weight residual 1.456 1.688 -0.232 1.22e-02 6.72e+03 3.61e+02 bond pdb=" C ALYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 1.334 1.114 0.220 1.20e-02 6.94e+03 3.38e+02 bond pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta sigma weight residual 1.456 1.235 0.221 1.26e-02 6.30e+03 3.08e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.236 1.419 -0.182 1.10e-02 8.26e+03 2.75e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 2932 4.25 - 8.50: 1862 8.50 - 12.74: 764 12.74 - 16.99: 190 16.99 - 21.24: 29 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ARG A 28 " pdb=" C ARG A 28 " pdb=" N ALA A 29 " ideal model delta sigma weight residual 122.12 138.52 -16.40 1.06e+00 8.90e-01 2.39e+02 angle pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 119.99 106.88 13.11 8.70e-01 1.32e+00 2.27e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 139.27 -16.07 1.08e+00 8.57e-01 2.21e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.22 105.67 16.55 1.17e+00 7.31e-01 2.00e+02 angle pdb=" O ASN A 81 " pdb=" C ASN A 81 " pdb=" N LEU A 82 " ideal model delta sigma weight residual 122.12 135.60 -13.48 1.06e+00 8.90e-01 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 1304 16.94 - 33.88: 119 33.88 - 50.81: 40 50.81 - 67.75: 16 67.75 - 84.69: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 25 " pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual -122.00 -141.71 19.71 0 2.50e+00 1.60e-01 6.22e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -141.96 19.36 0 2.50e+00 1.60e-01 6.00e+01 dihedral pdb=" C GLU A 176 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " pdb=" CB GLU A 176 " ideal model delta harmonic sigma weight residual -122.60 -141.30 18.70 0 2.50e+00 1.60e-01 5.60e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.194: 76 0.194 - 0.387: 73 0.387 - 0.580: 61 0.580 - 0.773: 21 0.773 - 0.966: 12 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 16 " pdb=" N GLU A 16 " pdb=" C GLU A 16 " pdb=" CB GLU A 16 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -3.53 0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.001 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.090 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.043 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.059 2.00e-02 2.50e+03 6.54e-02 9.62e+01 pdb=" CG HIS A 126 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.118 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.122 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " -0.049 2.00e-02 2.50e+03 7.85e-02 9.24e+01 pdb=" CG ASN A 173 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " 0.075 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " -0.120 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.075 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.38: 1486 2.38 - 2.93: 8395 2.93 - 3.49: 10385 3.49 - 4.04: 15036 4.04 - 4.60: 21272 Nonbonded interactions: 56574 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.823 2.450 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.829 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.832 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.845 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.863 2.450 ... (remaining 56569 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_3850167_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= 0.1811 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.412511 | | target function (ml) not normalized (work): 71672.417400 | | target function (ml) not normalized (free): 3245.019205 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3199 0.2133 7.6017 5.0275| | 2: 3.63 - 2.88 1.00 2711 122 0.2666 0.1773 4.3232 4.3273| | 3: 2.88 - 2.52 1.00 2682 148 0.2560 0.1683 4.1751 4.1762| | 4: 2.52 - 2.29 1.00 2661 139 0.2543 0.1497 3.5204 3.5766| | 5: 2.29 - 2.13 1.00 2678 122 0.2624 0.1486 3.3854 3.3979| | 6: 2.13 - 2.00 1.00 2692 117 0.2782 0.1794 3.3029 3.3158| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.49 0.77 0.23 1289.82| | 2: 3.63 - 2.88 2711 122 0.83 23.76 1.32 0.23 1289.82| | 3: 2.88 - 2.52 2682 148 0.73 32.80 1.29 0.23 1289.82| | 4: 2.52 - 2.29 2661 139 0.94 10.60 1.29 0.26 121.87| | 5: 2.29 - 2.13 2678 122 0.93 12.57 1.31 0.26 121.87| | 6: 2.13 - 2.00 2692 117 0.91 15.17 1.34 0.26 121.87| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 121.87 max = 1289.82 mean = 712.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.98 mean = 18.74| |phase err.(test): min = 0.00 max = 89.60 mean = 19.25| |-----------------------------------------------------------------------------| ----------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 0.233 1557 Z= 5.612 Angle : 5.255 16.549 2118 Z= 3.695 Chirality : 0.399 0.966 243 Planarity : 0.030 0.087 284 Dihedral : 13.955 84.687 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.27 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.46), residues: 224 helix: -2.82 (0.34), residues: 115 sheet: -0.73 (0.81), residues: 28 loop : 0.16 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.018 ARG A 98 TYR 0.084 0.034 TYR A 141 PHE 0.101 0.038 PHE A 162 HIS 0.086 0.052 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= 0.1811 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.412511 | | target function (ml) not normalized (work): 71672.417400 | | target function (ml) not normalized (free): 3245.019205 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3796 percent. r_work = 0.2932 r_free = 0.1988 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2878 0.2932 0.1988 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2878 0.2932 0.1988 n_refl.: 17050 remove outliers: r(all,work,free)=0.2174 0.2186 0.1988 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2147 0.2158 0.1968 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1628 0.1628 0.1627 n_refl.: 17045 remove outliers: r(all,work,free)=0.1627 0.1627 0.1627 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 0.4078 394.791 359.427 0.647 1.012 0.393 11.894-9.307 99.02 97 4 0.1812 633.652 617.809 0.932 1.012 0.370 9.237-7.194 100.00 213 7 0.2182 518.263 508.876 0.961 1.012 0.340 7.162-5.571 100.00 427 22 0.2329 388.957 375.932 0.919 1.010 0.279 5.546-4.326 100.00 867 58 0.1428 533.976 528.115 0.959 1.009 0.220 4.315-3.360 100.00 1859 96 0.1322 507.816 502.479 1.018 1.005 0.201 3.356-2.611 100.00 3867 181 0.1668 333.606 328.606 1.014 1.000 0.039 2.608-2.000 99.99 8818 434 0.1652 217.454 213.386 1.028 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4511 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1627 r_free=0.1627 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1627 r_free=0.1627 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.307669 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.859129 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 0.1353 0.1642 0.0289 0.009 1.0 1.6 0.5 0.0 0 11.654 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.42 2.89 3.013 18.452 0.859 0.023 12.79 16.62 3.83 3.608 18.714 0.859 0.020 Individual atomic B min max mean iso aniso Overall: 6.24 113.89 19.97 4.06 1785 0 Protein: 6.24 112.81 17.21 4.06 1519 0 Water: 8.71 113.89 36.06 N/A 258 0 Other: 22.05 37.14 26.45 N/A 8 0 Chain A: 6.24 113.89 19.97 N/A 1785 0 Histogram: Values Number of atoms 6.24 - 17.00 1091 17.00 - 27.77 335 27.77 - 38.53 186 38.53 - 49.30 98 49.30 - 60.07 48 60.07 - 70.83 13 70.83 - 81.60 6 81.60 - 92.36 4 92.36 - 103.13 1 103.13 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1662 r_work=0.1282 r_free=0.1669 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1669 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1276 r_free = 0.1661 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1276 r_free= 0.1661 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020029 | | target function (ls_wunit_k1) not normalized (work): 325.207545 | | target function (ls_wunit_k1) not normalized (free): 27.407980 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1276 0.1661 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1909 0.1908 0.1989 n_refl.: 17044 remove outliers: r(all,work,free)=0.1909 0.1908 0.1989 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1881 0.1879 0.1974 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1656 n_refl.: 17044 remove outliers: r(all,work,free)=0.1295 0.1277 0.1656 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 0.3668 301.408 281.147 0.621 1.010 0.367 11.894-9.307 99.02 97 4 0.1681 487.934 478.035 0.916 1.010 0.365 9.237-7.194 100.00 213 7 0.1817 399.081 396.724 0.959 1.010 0.348 7.162-5.571 100.00 427 22 0.1817 299.510 294.559 0.930 1.009 0.291 5.546-4.326 100.00 867 58 0.1047 411.180 408.799 0.958 1.007 0.205 4.315-3.360 100.00 1859 96 0.0930 391.036 390.629 1.018 1.004 0.191 3.356-2.611 100.00 3867 181 0.1301 256.888 255.602 1.016 1.000 0.091 2.608-2.000 99.99 8818 434 0.1353 167.447 165.958 1.023 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3993 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1656 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1656 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1656 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1285 r_free=0.1650 | n_water=252 | time (s): 20.100 (total time: 20.760) Filter (q & B) r_work=0.1285 r_free=0.1650 | n_water=250 | time (s): 1.650 (total time: 22.410) Compute maps r_work=0.1285 r_free=0.1650 | n_water=250 | time (s): 0.730 (total time: 23.140) Filter (map) r_work=0.1320 r_free=0.1636 | n_water=210 | time (s): 2.120 (total time: 25.260) Find peaks r_work=0.1320 r_free=0.1636 | n_water=210 | time (s): 0.650 (total time: 25.910) Add new water r_work=0.1539 r_free=0.1885 | n_water=372 | time (s): 1.800 (total time: 27.710) Refine new water occ: r_work=0.1332 r_free=0.1575 adp: r_work=0.1274 r_free=0.1583 occ: r_work=0.1281 r_free=0.1545 adp: r_work=0.1247 r_free=0.1558 occ: r_work=0.1247 r_free=0.1548 adp: r_work=0.1236 r_free=0.1550 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1550 r_work=0.1236 r_free=0.1550 | n_water=372 | time (s): 11.050 (total time: 38.760) Filter (q & B) r_work=0.1238 r_free=0.1553 | n_water=366 | time (s): 1.810 (total time: 40.570) Filter (dist only) r_work=0.1238 r_free=0.1554 | n_water=365 | time (s): 28.820 (total time: 69.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.836446 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.993394 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 0.1600 0.0392 0.008 0.9 3.8 0.5 0.0 0 12.418 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 16.00 3.92 4.165 21.091 0.993 0.018 11.92 16.28 4.35 4.194 21.369 0.993 0.018 Individual atomic B min max mean iso aniso Overall: 6.66 107.42 21.41 4.27 1892 0 Protein: 6.66 107.42 17.78 4.26 1519 0 Water: 8.35 68.16 36.23 N/A 365 0 Other: 25.13 44.54 34.45 N/A 8 0 Chain A: 6.66 107.42 19.49 N/A 1737 0 Chain S: 19.31 67.33 43.01 N/A 155 0 Histogram: Values Number of atoms 6.66 - 16.74 1023 16.74 - 26.81 385 26.81 - 36.89 216 36.89 - 46.97 163 46.97 - 57.04 65 57.04 - 67.12 27 67.12 - 77.19 6 77.19 - 87.27 3 87.27 - 97.35 2 97.35 - 107.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1628 r_work=0.1194 r_free=0.1629 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1629 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1628 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 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= 0.1189 r_free= 0.1628 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.016952 | | target function (ls_wunit_k1) not normalized (work): 275.230384 | | target function (ls_wunit_k1) not normalized (free): 25.086429 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1189 0.1628 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1815 0.1812 0.1949 n_refl.: 17043 remove outliers: r(all,work,free)=0.1815 0.1812 0.1949 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1789 0.1785 0.1932 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1184 0.1622 n_refl.: 17043 remove outliers: r(all,work,free)=0.1204 0.1183 0.1622 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 0.3497 303.377 277.515 0.597 1.006 0.364 11.894-9.307 99.02 97 4 0.1494 487.934 484.418 0.916 1.006 0.360 9.237-7.194 100.00 213 7 0.1664 399.081 399.769 0.976 1.006 0.290 7.162-5.571 100.00 427 22 0.1506 299.510 296.787 0.935 1.005 0.281 5.546-4.326 100.00 867 58 0.0866 411.180 408.930 0.958 1.005 0.210 4.315-3.360 100.00 1859 96 0.0823 391.036 390.021 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1182 256.888 256.049 1.011 1.001 0.121 2.608-2.000 99.99 8818 434 0.1330 167.447 166.434 1.016 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3416 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1183 r_free=0.1622 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1183 r_free=0.1622 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1622 | n_water=365 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1183 r_free=0.1623 | n_water=363 | time (s): 29.180 (total time: 29.850) Filter (q & B) r_work=0.1183 r_free=0.1623 | n_water=363 | time (s): 0.870 (total time: 30.720) Compute maps r_work=0.1183 r_free=0.1623 | n_water=363 | time (s): 0.680 (total time: 31.400) Filter (map) r_work=0.1251 r_free=0.1639 | n_water=263 | time (s): 1.940 (total time: 33.340) Find peaks r_work=0.1251 r_free=0.1639 | n_water=263 | time (s): 0.510 (total time: 33.850) Add new water r_work=0.1431 r_free=0.1808 | n_water=401 | time (s): 1.540 (total time: 35.390) Refine new water occ: r_work=0.1243 r_free=0.1557 adp: r_work=0.1233 r_free=0.1562 occ: r_work=0.1220 r_free=0.1542 adp: r_work=0.1208 r_free=0.1542 occ: r_work=0.1203 r_free=0.1530 adp: r_work=0.1192 r_free=0.1532 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1532 r_work=0.1192 r_free=0.1532 | n_water=401 | time (s): 34.600 (total time: 69.990) Filter (q & B) r_work=0.1194 r_free=0.1535 | n_water=396 | time (s): 1.860 (total time: 71.850) Filter (dist only) r_work=0.1194 r_free=0.1535 | n_water=396 | time (s): 29.920 (total time: 101.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.849476 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.195558 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1172 0.1536 0.0364 0.009 1.0 3.8 0.5 0.0 0 0.925 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.72 15.36 3.64 4.338 21.489 0.196 4.990 11.53 15.52 3.99 4.943 21.420 0.196 4.969 Individual atomic B min max mean iso aniso Overall: 6.43 105.99 20.82 4.85 1923 0 Protein: 6.43 105.99 17.07 4.84 1519 0 Water: 8.84 61.67 34.99 N/A 396 0 Other: 24.56 44.56 32.36 N/A 8 0 Chain A: 6.43 105.99 18.77 N/A 1734 0 Chain S: 16.18 61.67 39.61 N/A 189 0 Histogram: Values Number of atoms 6.43 - 16.39 1074 16.39 - 26.34 341 26.34 - 36.30 229 36.30 - 46.25 173 46.25 - 56.21 69 56.21 - 66.16 24 66.16 - 76.12 5 76.12 - 86.08 3 86.08 - 96.03 3 96.03 - 105.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1552 r_work=0.1153 r_free=0.1553 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1553 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1557 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.13 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= 0.1147 r_free= 0.1557 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.965262 | | target function (ml) not normalized (work): 80611.022382 | | target function (ml) not normalized (free): 4187.621226 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1147 0.1557 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1685 0.1679 0.1855 n_refl.: 17042 remove outliers: r(all,work,free)=0.1685 0.1679 0.1855 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1659 0.1652 0.1843 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1144 0.1557 n_refl.: 17042 remove outliers: r(all,work,free)=0.1164 0.1144 0.1557 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 0.3598 299.886 279.979 0.578 1.005 0.340 11.894-9.307 99.02 97 4 0.1740 487.934 481.017 0.917 1.006 0.340 9.237-7.194 100.00 213 7 0.1794 399.081 399.555 0.986 1.006 0.245 7.162-5.571 100.00 427 22 0.1636 299.510 294.211 0.939 1.006 0.231 5.546-4.326 100.00 867 58 0.0941 411.180 407.733 0.963 1.005 0.205 4.315-3.360 100.00 1859 96 0.0894 391.036 388.303 1.011 1.003 0.193 3.356-2.611 100.00 3867 181 0.1280 256.888 254.517 1.012 1.001 0.152 2.608-2.000 99.99 8818 434 0.1081 167.447 166.132 1.018 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3464 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1557 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1144 r_free=0.1557 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1557 | n_water=396 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1144 r_free=0.1559 | n_water=395 | time (s): 30.990 (total time: 31.760) Filter (q & B) r_work=0.1144 r_free=0.1560 | n_water=394 | time (s): 1.730 (total time: 33.490) Compute maps r_work=0.1144 r_free=0.1560 | n_water=394 | time (s): 0.740 (total time: 34.230) Filter (map) r_work=0.1198 r_free=0.1585 | n_water=313 | time (s): 1.770 (total time: 36.000) Find peaks r_work=0.1198 r_free=0.1585 | n_water=313 | time (s): 0.420 (total time: 36.420) Add new water r_work=0.1342 r_free=0.1712 | n_water=460 | time (s): 1.850 (total time: 38.270) Refine new water occ: r_work=0.1177 r_free=0.1502 adp: r_work=0.1168 r_free=0.1517 occ: r_work=0.1151 r_free=0.1481 adp: r_work=0.1141 r_free=0.1496 occ: r_work=0.1133 r_free=0.1471 adp: r_work=0.1125 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1125 r_free=0.1485 r_work=0.1125 r_free=0.1485 | n_water=460 | time (s): 20.310 (total time: 58.580) Filter (q & B) r_work=0.1129 r_free=0.1496 | n_water=451 | time (s): 2.250 (total time: 60.830) Filter (dist only) r_work=0.1129 r_free=0.1496 | n_water=450 | time (s): 36.440 (total time: 97.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.981918 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153666 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 0.1113 0.1557 0.0444 0.010 1.0 3.5 0.5 0.0 0 0.991 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.13 15.57 4.44 4.586 21.221 0.154 4.951 11.02 15.45 4.43 4.714 21.241 0.154 4.942 Individual atomic B min max mean iso aniso Overall: 5.82 102.56 21.18 4.87 1977 0 Protein: 5.82 102.56 16.59 4.87 1519 0 Water: 8.58 65.66 36.44 N/A 450 0 Other: 26.32 44.99 33.95 N/A 8 0 Chain A: 5.82 102.56 18.27 N/A 1734 0 Chain S: 15.72 65.66 41.92 N/A 243 0 Histogram: Values Number of atoms 5.82 - 15.50 1038 15.50 - 25.17 365 25.17 - 34.84 216 34.84 - 44.52 199 44.52 - 54.19 104 54.19 - 63.86 40 63.86 - 73.54 6 73.54 - 83.21 3 83.21 - 92.89 3 92.89 - 102.56 3 =========================== Idealize ADP of riding H ========================== r_work=0.1102 r_free=0.1545 r_work=0.1101 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1101 r_free = 0.1546 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1093 r_free = 0.1554 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1093 r_free= 0.1554 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.937833 | | target function (ml) not normalized (work): 80160.785336 | | target function (ml) not normalized (free): 4174.453648 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1116 0.1093 0.1554 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1583 0.1570 0.1868 n_refl.: 17041 remove outliers: r(all,work,free)=0.1583 0.1570 0.1868 n_refl.: 17041 overall B=-0.31 to atoms: r(all,work,free)=0.1563 0.1550 0.1858 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1113 0.1091 0.1548 n_refl.: 17041 remove outliers: r(all,work,free)=0.1113 0.1091 0.1548 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 0.3725 299.886 274.492 0.555 1.001 0.340 11.894-9.307 99.02 97 4 0.1686 487.934 482.502 0.922 1.002 0.340 9.237-7.194 100.00 213 7 0.1708 399.081 401.099 0.990 1.002 0.210 7.162-5.571 100.00 427 22 0.1551 299.510 292.919 0.938 1.002 0.205 5.546-4.326 100.00 867 58 0.0901 411.180 407.994 0.969 1.002 0.195 4.315-3.360 100.00 1859 96 0.0835 391.036 388.710 1.009 1.002 0.191 3.356-2.611 100.00 3867 181 0.1220 256.888 254.630 1.006 1.002 0.101 2.608-2.000 99.99 8818 434 0.1036 167.447 166.297 1.003 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0728 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1091 r_free=0.1548 After: r_work=0.1094 r_free=0.1547 ================================== NQH flips ================================== r_work=0.1094 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1094 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1094 r_free=0.1547 | n_water=450 | time (s): 0.750 (total time: 0.750) Filter (dist) r_work=0.1097 r_free=0.1547 | n_water=449 | time (s): 37.370 (total time: 38.120) Filter (q & B) r_work=0.1097 r_free=0.1547 | n_water=449 | time (s): 1.130 (total time: 39.250) Compute maps r_work=0.1097 r_free=0.1547 | n_water=449 | time (s): 0.700 (total time: 39.950) Filter (map) r_work=0.1170 r_free=0.1558 | n_water=343 | time (s): 1.720 (total time: 41.670) Find peaks r_work=0.1170 r_free=0.1558 | n_water=343 | time (s): 0.420 (total time: 42.090) Add new water r_work=0.1281 r_free=0.1651 | n_water=480 | time (s): 1.530 (total time: 43.620) Refine new water occ: r_work=0.1127 r_free=0.1516 adp: r_work=0.1120 r_free=0.1519 occ: r_work=0.1108 r_free=0.1498 adp: r_work=0.1099 r_free=0.1502 occ: r_work=0.1093 r_free=0.1489 adp: r_work=0.1088 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1088 r_free=0.1494 r_work=0.1088 r_free=0.1494 | n_water=480 | time (s): 20.780 (total time: 64.400) Filter (q & B) r_work=0.1090 r_free=0.1507 | n_water=469 | time (s): 1.780 (total time: 66.180) Filter (dist only) r_work=0.1090 r_free=0.1508 | n_water=468 | time (s): 38.440 (total time: 104.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.904641 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.142548 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 0.1114 0.1518 0.0405 0.009 1.0 5.8 0.5 0.0 0 0.952 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.14 15.18 4.05 4.561 20.913 0.143 4.939 11.06 15.10 4.04 4.620 21.022 0.143 4.932 Individual atomic B min max mean iso aniso Overall: 5.69 99.54 21.18 4.97 1995 0 Protein: 5.69 99.54 16.35 4.97 1519 0 Water: 8.02 67.55 36.67 N/A 468 0 Other: 25.32 42.56 31.99 N/A 8 0 Chain A: 5.69 99.54 18.00 N/A 1733 0 Chain S: 17.27 67.55 42.22 N/A 262 0 Histogram: Values Number of atoms 5.69 - 15.08 1019 15.08 - 24.46 382 24.46 - 33.85 212 33.85 - 43.23 194 43.23 - 52.61 126 52.61 - 62.00 39 62.00 - 71.38 13 71.38 - 80.77 1 80.77 - 90.15 5 90.15 - 99.54 4 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1510 r_work=0.1106 r_free=0.1511 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1511 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1506 target_work(ml) = 4.927 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1099 r_free= 0.1506 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.927312 | | target function (ml) not normalized (work): 79989.982882 | | target function (ml) not normalized (free): 4162.532953 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1114 0.1445 5.4489 5.6691| | 2: 3.63 - 2.88 1.00 2711 122 0.1078 0.1410 5.2129 5.3504| | 3: 2.88 - 2.52 1.00 2681 148 0.1333 0.1632 5.1287 5.1832| | 4: 2.52 - 2.29 1.00 2661 139 0.0926 0.1458 4.6141 4.9103| | 5: 2.29 - 2.13 1.00 2678 122 0.0966 0.1545 4.567 4.9075| | 6: 2.13 - 2.00 1.00 2692 117 0.1124 0.1749 4.5624 4.7867| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2811 159 0.94 9.12 1.00 0.96 6431.60| | 2: 3.63 - 2.88 2711 122 0.92 12.87 1.01 0.96 6431.60| | 3: 2.88 - 2.52 2681 148 0.87 19.05 0.99 0.96 6431.60| | 4: 2.52 - 2.29 2661 139 0.93 11.73 1.01 0.98 2033.97| | 5: 2.29 - 2.13 2678 122 0.92 13.79 1.00 0.98 2033.97| | 6: 2.13 - 2.00 2692 117 0.90 16.51 0.99 0.98 2033.97| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2033.97 max = 6431.60 mean = 4256.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.90 mean = 13.81| |phase err.(test): min = 0.00 max = 88.83 mean = 13.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1099 0.1506 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1574 0.1563 0.1809 n_refl.: 17041 remove outliers: r(all,work,free)=0.1574 0.1563 0.1809 n_refl.: 17041 overall B=-0.27 to atoms: r(all,work,free)=0.1557 0.1546 0.1800 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1101 0.1503 n_refl.: 17041 remove outliers: r(all,work,free)=0.1121 0.1101 0.1503 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3660 299.886 278.932 0.536 1.003 0.308 11.894-9.307 99.02 97 4 0.1805 487.934 480.180 0.918 1.005 0.292 9.237-7.194 100.00 213 7 0.1779 399.081 401.449 0.985 1.005 0.228 7.162-5.571 100.00 427 22 0.1585 299.510 293.485 0.931 1.004 0.203 5.546-4.326 100.00 867 58 0.0920 411.180 407.855 0.966 1.004 0.181 4.315-3.360 100.00 1859 96 0.0859 391.036 388.818 1.006 1.003 0.181 3.356-2.611 100.00 3867 181 0.1222 256.888 254.714 1.005 1.001 0.101 2.608-2.000 99.99 8818 434 0.1034 167.447 166.218 0.999 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9277 ================= 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 0.1811 0.084 5.255 8.8 119.3 19.9 258 0.000 1_bss: 0.1627 0.1627 0.084 5.255 8.4 118.9 19.5 258 0.000 1_settarget: 0.1627 0.1627 0.084 5.255 8.4 118.9 19.5 258 0.000 1_nqh: 0.1627 0.1627 0.084 5.255 8.4 118.9 19.5 258 0.000 1_weight: 0.1627 0.1627 0.084 5.255 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1353 0.1642 0.009 0.969 8.4 118.9 19.5 258 0.148 1_adp: 0.1279 0.1662 0.009 0.969 6.2 113.9 20.0 258 0.148 1_regHadp: 0.1282 0.1669 0.009 0.969 6.2 113.9 20.0 258 0.148 1_occ: 0.1276 0.1661 0.009 0.969 6.2 113.9 20.0 258 0.148 2_bss: 0.1277 0.1656 0.009 0.969 5.8 113.5 19.6 258 0.148 2_settarget: 0.1277 0.1656 0.009 0.969 5.8 113.5 19.6 258 0.148 2_updatecdl: 0.1277 0.1656 0.009 0.984 5.8 113.5 19.6 258 0.148 2_nqh: 0.1277 0.1656 0.009 0.984 5.8 113.5 19.6 258 0.148 2_sol: 0.1238 0.1554 0.009 0.984 5.8 112.4 20.9 365 n/a 2_weight: 0.1238 0.1554 0.009 0.984 5.8 112.4 20.9 365 n/a 2_xyzrec: 0.1208 0.1600 0.008 0.929 5.8 112.4 20.9 365 n/a 2_adp: 0.1192 0.1628 0.008 0.929 6.7 107.4 21.4 365 n/a 2_regHadp: 0.1194 0.1629 0.008 0.929 6.7 107.4 21.4 365 n/a 2_occ: 0.1189 0.1628 0.008 0.929 6.7 107.4 21.4 365 n/a 3_bss: 0.1183 0.1622 0.008 0.929 6.3 107.0 21.0 365 n/a 3_settarget: 0.1183 0.1622 0.008 0.929 6.3 107.0 21.0 365 n/a 3_updatecdl: 0.1183 0.1622 0.008 0.931 6.3 107.0 21.0 365 n/a 3_nqh: 0.1183 0.1622 0.008 0.931 6.3 107.0 21.0 365 n/a 3_sol: 0.1194 0.1535 0.008 0.931 6.3 107.0 20.9 396 n/a 3_weight: 0.1194 0.1535 0.008 0.931 6.3 107.0 20.9 396 n/a 3_xyzrec: 0.1172 0.1536 0.009 0.958 6.3 107.0 20.9 396 n/a 3_adp: 0.1153 0.1552 0.009 0.958 6.4 106.0 20.8 396 n/a 3_regHadp: 0.1153 0.1553 0.009 0.958 6.4 106.0 20.8 396 n/a 3_occ: 0.1147 0.1557 0.009 0.958 6.4 106.0 20.8 396 n/a 4_bss: 0.1144 0.1557 0.009 0.958 6.1 105.6 20.4 396 n/a 4_settarget: 0.1144 0.1557 0.009 0.958 6.1 105.6 20.4 396 n/a 4_updatecdl: 0.1144 0.1557 0.009 0.957 6.1 105.6 20.4 396 n/a 4_nqh: 0.1144 0.1557 0.009 0.957 6.1 105.6 20.4 396 n/a 4_sol: 0.1129 0.1496 0.009 0.957 6.1 105.6 21.1 450 n/a 4_weight: 0.1129 0.1496 0.009 0.957 6.1 105.6 21.1 450 n/a 4_xyzrec: 0.1113 0.1557 0.010 0.989 6.1 105.6 21.1 450 n/a 4_adp: 0.1102 0.1545 0.010 0.989 5.8 102.6 21.2 450 n/a 4_regHadp: 0.1101 0.1546 0.010 0.989 5.8 102.6 21.2 450 n/a 4_occ: 0.1093 0.1554 0.010 0.989 5.8 102.6 21.2 450 n/a 5_bss: 0.1091 0.1548 0.010 0.989 5.5 102.2 20.9 450 n/a 5_settarget: 0.1091 0.1548 0.010 0.989 5.5 102.2 20.9 450 n/a 5_updatecdl: 0.1091 0.1548 0.010 0.990 5.5 102.2 20.9 450 n/a 5_setrh: 0.1094 0.1547 0.010 0.990 5.5 102.2 20.9 450 n/a 5_nqh: 0.1094 0.1547 0.010 0.990 5.5 102.2 20.9 450 n/a 5_sol: 0.1090 0.1508 0.010 0.990 5.5 102.2 21.0 468 n/a 5_weight: 0.1090 0.1508 0.010 0.990 5.5 102.2 21.0 468 n/a 5_xyzrec: 0.1114 0.1518 0.009 1.035 5.5 102.2 21.0 468 n/a 5_adp: 0.1106 0.1510 0.009 1.035 5.7 99.5 21.2 468 n/a 5_regHadp: 0.1106 0.1511 0.009 1.035 5.7 99.5 21.2 468 n/a 5_occ: 0.1099 0.1506 0.009 1.035 5.7 99.5 21.2 468 n/a end: 0.1101 0.1503 0.009 1.035 5.4 99.3 20.9 468 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3850167_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3850167_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5700 Refinement macro-cycles (run) : 907.0700 Write final files (write_after_run_outputs) : 20.0700 Total : 930.7100 Total CPU time: 15.84 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:52 PST -0800 (1735494052.55 s) Start R-work = 0.1627, R-free = 0.1627 Final R-work = 0.1101, R-free = 0.1503 =============================================================================== Job complete usr+sys time: 974.13 seconds wall clock time: 16 minutes 37.49 seconds (997.49 seconds total)