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_9255201.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9255201.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9255201.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.84, per 1000 atoms: 0.54 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: 0.51 Conformation dependent library (CDL) restraints added in 186.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.93: 647 0.93 - 1.19: 1037 1.19 - 1.46: 743 1.46 - 1.72: 709 1.72 - 1.98: 17 Bond restraints: 3153 Sorted by residual: bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.520 1.342 0.178 7.00e-03 2.04e+04 6.43e+02 bond pdb=" N BLEU A 153 " pdb=" CA BLEU A 153 " ideal model delta sigma weight residual 1.456 1.687 -0.230 1.21e-02 6.83e+03 3.62e+02 bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 1.025 0.211 1.14e-02 7.69e+03 3.41e+02 bond pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 1.461 1.666 -0.206 1.19e-02 7.06e+03 2.99e+02 bond pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta sigma weight residual 1.459 1.676 -0.218 1.28e-02 6.10e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 3405 5.16 - 10.31: 1802 10.31 - 15.47: 494 15.47 - 20.62: 69 20.62 - 25.78: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.38 105.91 15.47 8.20e-01 1.49e+00 3.56e+02 angle pdb=" CA HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 118.83 131.47 -12.64 8.70e-01 1.32e+00 2.11e+02 angle pdb=" O VAL A 23 " pdb=" C VAL A 23 " pdb=" N ASP A 24 " ideal model delta sigma weight residual 121.94 136.77 -14.83 1.03e+00 9.43e-01 2.07e+02 angle pdb=" OE1 GLN A 95 " pdb=" CD GLN A 95 " pdb=" NE2 GLN A 95 " ideal model delta sigma weight residual 122.60 136.83 -14.23 1.00e+00 1.00e+00 2.03e+02 angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 131.68 -12.48 9.00e-01 1.23e+00 1.92e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 1287 16.03 - 32.06: 127 32.06 - 48.09: 47 48.09 - 64.12: 17 64.12 - 80.15: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 69 " pdb=" N VAL A 69 " pdb=" CA VAL A 69 " pdb=" CB VAL A 69 " ideal model delta harmonic sigma weight residual -122.00 -141.43 19.43 0 2.50e+00 1.60e-01 6.04e+01 dihedral pdb=" C GLU A 59 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " pdb=" CB GLU A 59 " ideal model delta harmonic sigma weight residual -122.60 -141.77 19.17 0 2.50e+00 1.60e-01 5.88e+01 dihedral pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CA GLU A 59 " pdb=" CB GLU A 59 " ideal model delta harmonic sigma weight residual 122.80 141.11 -18.31 0 2.50e+00 1.60e-01 5.36e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 106 0.219 - 0.438: 72 0.438 - 0.657: 38 0.657 - 0.876: 19 0.876 - 1.095: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -3.72 1.09 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.53 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA BGLU A 64 " pdb=" N BGLU A 64 " pdb=" C BGLU A 64 " pdb=" CB BGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.072 2.00e-02 2.50e+03 7.07e-02 1.13e+02 pdb=" CG HIS A 115 " 0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.096 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.098 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.034 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.005 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG BTYR A 67 " -0.013 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.100 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.109 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.060 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " 0.201 9.50e-02 1.11e+02 8.74e-02 7.56e+01 pdb=" NE ARG A 145 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.082 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.016 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " 0.081 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.065 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " 0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 760 2.28 - 2.86: 7840 2.86 - 3.44: 10641 3.44 - 4.02: 15227 4.02 - 4.60: 22108 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.696 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.736 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.763 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.837 2.100 nonbonded pdb=" H GLU A 147 " pdb=" O THR A 154 " model vdw 1.837 2.450 ... (remaining 56571 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_9255201_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= 0.2782 r_free= 0.1788 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.414509 | | target function (ml) not normalized (work): 71704.865846 | | target function (ml) not normalized (free): 3263.072836 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3195 0.2140 7.5909 5.0367| | 2: 3.63 - 2.88 1.00 2711 122 0.2641 0.1613 4.3259 4.2996| | 3: 2.88 - 2.52 1.00 2682 148 0.2555 0.1715 4.1776 4.1813| | 4: 2.52 - 2.29 1.00 2661 139 0.2577 0.1428 3.5164 3.5766| | 5: 2.29 - 2.13 1.00 2678 122 0.2625 0.1374 3.3934 3.3908| | 6: 2.13 - 2.00 1.00 2692 117 0.2688 0.2041 3.3172 3.4874| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.37 0.77 0.23 1276.12| | 2: 3.63 - 2.88 2711 122 0.83 23.66 1.32 0.23 1276.12| | 3: 2.88 - 2.52 2682 148 0.74 32.53 1.28 0.23 1276.12| | 4: 2.52 - 2.29 2661 139 0.93 11.54 1.30 0.26 137.85| | 5: 2.29 - 2.13 2678 122 0.92 13.87 1.31 0.26 137.85| | 6: 2.13 - 2.00 2692 117 0.90 16.49 1.33 0.26 137.85| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 137.85 max = 1276.12 mean = 713.32| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.97 mean = 19.25| |phase err.(test): min = 0.00 max = 89.53 mean = 19.50| |-----------------------------------------------------------------------------| ----------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 0.303 1557 Z= 5.547 Angle : 5.376 15.872 2118 Z= 3.761 Chirality : 0.394 1.095 243 Planarity : 0.029 0.122 284 Dihedral : 13.828 80.154 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 31.35 % 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: -2.41 (0.48), residues: 224 helix: -2.71 (0.35), residues: 109 sheet: 0.13 (1.00), residues: 28 loop : -0.30 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.094 0.020 ARG A 27 TYR 0.049 0.023 TYR A 139 PHE 0.103 0.039 PHE A 119 HIS 0.056 0.029 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= 0.2782 r_free= 0.1788 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.414509 | | target function (ml) not normalized (work): 71704.865846 | | target function (ml) not normalized (free): 3263.072836 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3164 percent. r_work = 0.2913 r_free = 0.1964 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2859 0.2913 0.1964 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2859 0.2913 0.1964 n_refl.: 17050 remove outliers: r(all,work,free)=0.2148 0.2159 0.1964 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2122 0.2133 0.1947 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1615 0.1615 0.1623 n_refl.: 17045 remove outliers: r(all,work,free)=0.1612 0.1612 0.1623 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 97.87 87 5 0.3963 393.890 353.896 0.628 1.006 0.370 11.894-9.307 99.02 97 4 0.1827 633.510 619.069 0.939 1.007 0.370 9.237-7.194 100.00 213 7 0.2190 518.147 509.359 0.961 1.007 0.360 7.162-5.571 100.00 427 22 0.2329 388.870 376.192 0.928 1.006 0.298 5.546-4.326 100.00 867 58 0.1395 533.856 527.882 0.966 1.005 0.225 4.315-3.360 100.00 1859 96 0.1302 507.702 503.798 1.019 1.004 0.201 3.356-2.611 100.00 3867 181 0.1646 333.532 329.124 1.015 1.001 0.061 2.608-2.000 99.99 8818 434 0.1650 217.405 213.124 1.023 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-1.4504 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1612 r_free=0.1623 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1614 r_free=0.1623 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.041695 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.837518 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1349 0.1639 0.0290 0.009 1.0 0.6 0.5 0.0 0 11.521 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.39 2.90 3.012 18.451 0.838 0.023 12.75 16.63 3.88 3.601 18.718 0.838 0.020 Individual atomic B min max mean iso aniso Overall: 6.54 113.89 19.98 4.04 1785 0 Protein: 6.54 112.44 17.23 4.04 1519 0 Water: 8.84 113.89 36.02 N/A 258 0 Other: 21.86 37.06 26.42 N/A 8 0 Chain A: 6.54 113.89 19.98 N/A 1785 0 Histogram: Values Number of atoms 6.54 - 17.27 1096 17.27 - 28.01 337 28.01 - 38.74 180 38.74 - 49.48 99 49.48 - 60.21 47 60.21 - 70.95 13 70.95 - 81.69 5 81.69 - 92.42 4 92.42 - 103.16 1 103.16 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1275 r_free=0.1663 r_work=0.1278 r_free=0.1670 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1278 r_free = 0.1670 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 = 0.1273 r_free = 0.1664 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1273 r_free= 0.1664 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019842 | | target function (ls_wunit_k1) not normalized (work): 322.136631 | | target function (ls_wunit_k1) not normalized (free): 27.055348 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1292 0.1273 0.1664 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1852 0.1847 0.2001 n_refl.: 17042 remove outliers: r(all,work,free)=0.1852 0.1847 0.2001 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1827 0.1820 0.1985 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1288 0.1270 0.1657 n_refl.: 17042 remove outliers: r(all,work,free)=0.1288 0.1270 0.1657 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 0.3504 303.328 282.590 0.620 1.004 0.360 11.894-9.307 99.02 97 4 0.1693 487.855 476.527 0.917 1.005 0.359 9.237-7.194 100.00 213 7 0.1780 399.016 395.668 0.960 1.005 0.341 7.162-5.571 100.00 427 22 0.1833 299.462 294.132 0.933 1.005 0.301 5.546-4.326 100.00 867 58 0.1036 411.114 408.428 0.959 1.004 0.210 4.315-3.360 100.00 1859 96 0.0920 390.973 390.311 1.015 1.003 0.191 3.356-2.611 100.00 3867 181 0.1295 256.847 255.541 1.013 1.001 0.091 2.608-2.000 99.99 8818 434 0.1349 167.420 166.116 1.017 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3581 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1270 r_free=0.1657 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1272 r_free=0.1657 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1657 | n_water=258 | time (s): 0.820 (total time: 0.820) Filter (dist) r_work=0.1280 r_free=0.1644 | n_water=253 | time (s): 22.540 (total time: 23.360) Filter (q & B) r_work=0.1280 r_free=0.1644 | n_water=251 | time (s): 1.910 (total time: 25.270) Compute maps r_work=0.1280 r_free=0.1644 | n_water=251 | time (s): 0.830 (total time: 26.100) Filter (map) r_work=0.1310 r_free=0.1640 | n_water=215 | time (s): 1.940 (total time: 28.040) Find peaks r_work=0.1310 r_free=0.1640 | n_water=215 | time (s): 0.550 (total time: 28.590) Add new water r_work=0.1530 r_free=0.1870 | n_water=373 | time (s): 2.170 (total time: 30.760) Refine new water occ: r_work=0.1328 r_free=0.1577 adp: r_work=0.1271 r_free=0.1574 occ: r_work=0.1274 r_free=0.1547 adp: r_work=0.1242 r_free=0.1556 occ: r_work=0.1241 r_free=0.1543 adp: r_work=0.1229 r_free=0.1546 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1546 r_work=0.1229 r_free=0.1546 | n_water=373 | time (s): 13.600 (total time: 44.360) Filter (q & B) r_work=0.1231 r_free=0.1552 | n_water=364 | time (s): 2.070 (total time: 46.430) Filter (dist only) r_work=0.1230 r_free=0.1556 | n_water=363 | time (s): 28.800 (total time: 75.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.804831 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.974801 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 0.1202 0.1593 0.0392 0.008 0.9 2.6 0.5 0.0 0 12.402 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 15.93 3.92 4.152 21.143 0.975 0.018 11.90 16.08 4.18 4.184 21.455 0.975 0.017 Individual atomic B min max mean iso aniso Overall: 6.81 107.06 21.55 4.27 1890 0 Protein: 6.81 107.06 17.86 4.25 1519 0 Water: 8.76 68.17 36.69 N/A 363 0 Other: 23.72 44.97 34.29 N/A 8 0 Chain A: 6.81 107.06 19.66 N/A 1742 0 Chain S: 18.03 61.50 43.76 N/A 148 0 Histogram: Values Number of atoms 6.81 - 16.84 1017 16.84 - 26.86 376 26.86 - 36.89 216 36.89 - 46.91 172 46.91 - 56.94 73 56.94 - 66.96 24 66.96 - 76.99 4 76.99 - 87.01 5 87.01 - 97.04 1 97.04 - 107.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1608 r_work=0.1192 r_free=0.1609 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1609 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1610 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.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1190 r_free= 0.1610 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016882 | | target function (ls_wunit_k1) not normalized (work): 274.083874 | | target function (ls_wunit_k1) not normalized (free): 24.693532 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1190 0.1610 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1762 0.1753 0.1972 n_refl.: 17042 remove outliers: r(all,work,free)=0.1762 0.1753 0.1972 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1736 0.1726 0.1954 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1186 0.1603 n_refl.: 17042 remove outliers: r(all,work,free)=0.1206 0.1186 0.1603 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 0.3306 303.328 283.802 0.603 1.005 0.350 11.894-9.307 99.02 97 4 0.1469 487.855 485.856 0.913 1.006 0.340 9.237-7.194 100.00 213 7 0.1682 399.016 400.200 0.974 1.006 0.290 7.162-5.571 100.00 427 22 0.1548 299.462 296.206 0.934 1.005 0.271 5.546-4.326 100.00 867 58 0.0860 411.114 408.403 0.960 1.005 0.211 4.315-3.360 100.00 1859 96 0.0835 390.973 390.326 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1200 256.847 256.140 1.014 1.000 0.121 2.608-2.000 99.99 8818 434 0.1321 167.420 166.346 1.021 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4075 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1603 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1186 r_free=0.1603 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1603 | n_water=363 | time (s): 0.840 (total time: 0.840) Filter (dist) r_work=0.1186 r_free=0.1605 | n_water=362 | time (s): 28.820 (total time: 29.660) Filter (q & B) r_work=0.1186 r_free=0.1605 | n_water=362 | time (s): 1.090 (total time: 30.750) Compute maps r_work=0.1186 r_free=0.1605 | n_water=362 | time (s): 0.800 (total time: 31.550) Filter (map) r_work=0.1252 r_free=0.1608 | n_water=264 | time (s): 2.130 (total time: 33.680) Find peaks r_work=0.1252 r_free=0.1608 | n_water=264 | time (s): 0.600 (total time: 34.280) Add new water r_work=0.1438 r_free=0.1760 | n_water=411 | time (s): 2.110 (total time: 36.390) Refine new water occ: r_work=0.1251 r_free=0.1563 adp: r_work=0.1242 r_free=0.1568 occ: r_work=0.1224 r_free=0.1536 adp: r_work=0.1212 r_free=0.1540 occ: r_work=0.1204 r_free=0.1519 adp: r_work=0.1194 r_free=0.1522 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1522 r_work=0.1194 r_free=0.1522 | n_water=411 | time (s): 33.920 (total time: 70.310) Filter (q & B) r_work=0.1198 r_free=0.1526 | n_water=402 | time (s): 2.130 (total time: 72.440) Filter (dist only) r_work=0.1198 r_free=0.1527 | n_water=401 | time (s): 31.860 (total time: 104.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.789118 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.142807 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 0.1176 0.1535 0.0359 0.009 1.0 4.5 0.5 0.0 0 0.895 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 15.35 3.59 4.342 21.666 0.143 4.986 11.55 15.53 3.98 4.851 21.573 0.143 4.965 Individual atomic B min max mean iso aniso Overall: 6.59 104.30 21.02 4.61 1928 0 Protein: 6.59 104.30 17.13 4.61 1519 0 Water: 8.10 63.23 35.50 N/A 401 0 Other: 26.03 45.68 34.22 N/A 8 0 Chain A: 6.59 104.30 18.88 N/A 1737 0 Chain S: 14.37 63.23 40.51 N/A 191 0 Histogram: Values Number of atoms 6.59 - 16.36 1068 16.36 - 26.13 345 26.13 - 35.90 225 35.90 - 45.67 174 45.67 - 55.44 71 55.44 - 65.21 32 65.21 - 74.99 5 74.99 - 84.76 3 84.76 - 94.53 3 94.53 - 104.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1553 r_work=0.1155 r_free=0.1553 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1155 r_free = 0.1553 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1546 target_work(ml) = 4.958 | | occupancies: max = 1.00 min = 0.21 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= 0.1145 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.958400 | | target function (ml) not normalized (work): 80499.622784 | | target function (ml) not normalized (free): 4174.161612 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1164 0.1145 0.1546 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1675 0.1668 0.1864 n_refl.: 17042 remove outliers: r(all,work,free)=0.1675 0.1668 0.1864 n_refl.: 17042 overall B=-0.40 to atoms: r(all,work,free)=0.1646 0.1638 0.1849 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1163 0.1143 0.1545 n_refl.: 17042 remove outliers: r(all,work,free)=0.1162 0.1142 0.1545 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 0.3573 299.838 279.753 0.575 1.003 0.350 11.894-9.307 99.02 97 4 0.1800 487.855 479.630 0.909 1.004 0.350 9.237-7.194 100.00 213 7 0.1843 399.016 400.325 0.990 1.004 0.255 7.162-5.571 100.00 427 22 0.1621 299.462 294.454 0.941 1.004 0.251 5.546-4.326 100.00 867 58 0.0951 411.114 407.752 0.965 1.003 0.196 4.315-3.360 100.00 1859 96 0.0888 390.973 388.581 1.013 1.003 0.191 3.356-2.611 100.00 3867 181 0.1269 256.847 254.757 1.014 1.001 0.142 2.608-2.000 99.99 8818 434 0.1083 167.420 166.107 1.018 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4281 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1142 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1545 | n_water=401 | time (s): 0.880 (total time: 0.880) Filter (dist) r_work=0.1142 r_free=0.1545 | n_water=401 | time (s): 31.250 (total time: 32.130) Filter (q & B) r_work=0.1142 r_free=0.1545 | n_water=401 | time (s): 1.220 (total time: 33.350) Compute maps r_work=0.1142 r_free=0.1545 | n_water=401 | time (s): 0.780 (total time: 34.130) Filter (map) r_work=0.1192 r_free=0.1555 | n_water=317 | time (s): 1.660 (total time: 35.790) Find peaks r_work=0.1192 r_free=0.1555 | n_water=317 | time (s): 0.450 (total time: 36.240) Add new water r_work=0.1321 r_free=0.1720 | n_water=460 | time (s): 1.600 (total time: 37.840) Refine new water occ: r_work=0.1164 r_free=0.1539 adp: r_work=0.1159 r_free=0.1544 occ: r_work=0.1140 r_free=0.1518 adp: r_work=0.1133 r_free=0.1523 occ: r_work=0.1124 r_free=0.1506 adp: r_work=0.1117 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1117 r_free=0.1510 r_work=0.1117 r_free=0.1510 | n_water=460 | time (s): 29.610 (total time: 67.450) Filter (q & B) r_work=0.1121 r_free=0.1514 | n_water=449 | time (s): 1.410 (total time: 68.860) Filter (dist only) r_work=0.1121 r_free=0.1512 | n_water=448 | time (s): 35.540 (total time: 104.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.841649 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150017 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 0.1111 0.1554 0.0443 0.009 1.0 5.8 0.5 0.0 0 0.921 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.11 15.54 4.43 4.460 21.232 0.150 4.950 11.01 15.54 4.53 4.686 21.213 0.150 4.941 Individual atomic B min max mean iso aniso Overall: 6.18 102.07 21.09 4.83 1975 0 Protein: 6.18 102.07 16.62 4.82 1519 0 Water: 8.37 63.05 36.03 N/A 448 0 Other: 25.47 45.04 33.21 N/A 8 0 Chain A: 6.18 102.07 18.30 N/A 1735 0 Chain S: 17.61 63.05 41.28 N/A 240 0 Histogram: Values Number of atoms 6.18 - 15.77 1050 15.77 - 25.36 361 25.36 - 34.95 218 34.95 - 44.54 192 44.54 - 54.13 102 54.13 - 63.71 38 63.71 - 73.30 5 73.30 - 82.89 4 82.89 - 92.48 3 92.48 - 102.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1101 r_free=0.1554 r_work=0.1101 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1101 r_free = 0.1554 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1093 r_free = 0.1547 target_work(ml) = 4.937 | | 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.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1093 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.936817 | | target function (ml) not normalized (work): 80144.280832 | | target function (ml) not normalized (free): 4173.862980 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1115 0.1093 0.1547 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1588 0.1577 0.1827 n_refl.: 17041 remove outliers: r(all,work,free)=0.1588 0.1577 0.1827 n_refl.: 17041 overall B=-0.31 to atoms: r(all,work,free)=0.1567 0.1556 0.1816 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1112 0.1090 0.1542 n_refl.: 17041 remove outliers: r(all,work,free)=0.1111 0.1089 0.1542 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 0.3664 296.603 275.634 0.554 1.003 0.340 11.894-9.307 99.02 97 4 0.1758 487.855 482.193 0.912 1.004 0.336 9.237-7.194 100.00 213 7 0.1760 399.016 400.827 0.990 1.004 0.250 7.162-5.571 100.00 427 22 0.1490 299.462 294.309 0.940 1.004 0.195 5.546-4.326 100.00 867 58 0.0904 411.114 407.663 0.965 1.004 0.191 4.315-3.360 100.00 1859 96 0.0841 390.973 388.340 1.008 1.003 0.191 3.356-2.611 100.00 3867 181 0.1215 256.847 254.820 1.007 1.001 0.121 2.608-2.000 99.99 8818 434 0.1032 167.420 166.299 1.006 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0844 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1089 r_free=0.1542 After: r_work=0.1091 r_free=0.1541 ================================== NQH flips ================================== r_work=0.1091 r_free=0.1541 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1091 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1091 r_free=0.1541 | n_water=448 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1091 r_free=0.1541 | n_water=448 | time (s): 35.170 (total time: 35.880) Filter (q & B) r_work=0.1091 r_free=0.1541 | n_water=448 | time (s): 0.820 (total time: 36.700) Compute maps r_work=0.1091 r_free=0.1541 | n_water=448 | time (s): 0.720 (total time: 37.420) Filter (map) r_work=0.1167 r_free=0.1554 | n_water=343 | time (s): 1.910 (total time: 39.330) Find peaks r_work=0.1167 r_free=0.1554 | n_water=343 | time (s): 0.640 (total time: 39.970) Add new water r_work=0.1273 r_free=0.1642 | n_water=469 | time (s): 1.910 (total time: 41.880) Refine new water occ: r_work=0.1135 r_free=0.1525 adp: r_work=0.1131 r_free=0.1526 occ: r_work=0.1115 r_free=0.1506 adp: r_work=0.1109 r_free=0.1509 occ: r_work=0.1102 r_free=0.1491 adp: r_work=0.1096 r_free=0.1492 ADP+occupancy (water only), MIN, final r_work=0.1096 r_free=0.1492 r_work=0.1096 r_free=0.1492 | n_water=469 | time (s): 38.550 (total time: 80.430) Filter (q & B) r_work=0.1102 r_free=0.1500 | n_water=451 | time (s): 1.630 (total time: 82.060) Filter (dist only) r_work=0.1102 r_free=0.1501 | n_water=450 | time (s): 37.080 (total time: 119.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.935858 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.149050 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 0.1522 0.0404 0.009 1.0 5.4 0.5 0.0 0 0.968 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 15.22 4.04 4.534 20.849 0.149 4.943 11.10 15.21 4.10 4.613 20.858 0.149 4.939 Individual atomic B min max mean iso aniso Overall: 5.61 101.16 20.86 4.96 1977 0 Protein: 5.61 101.16 16.26 4.95 1519 0 Water: 7.84 66.51 36.19 N/A 450 0 Other: 26.20 44.54 33.01 N/A 8 0 Chain A: 5.61 101.16 17.92 N/A 1735 0 Chain S: 17.89 66.51 41.99 N/A 242 0 Histogram: Values Number of atoms 5.61 - 15.17 1029 15.17 - 24.72 376 24.72 - 34.27 207 34.27 - 43.83 193 43.83 - 53.38 120 53.38 - 62.94 34 62.94 - 72.49 9 72.49 - 82.05 3 82.05 - 91.60 3 91.60 - 101.16 3 =========================== Idealize ADP of riding H ========================== r_work=0.1110 r_free=0.1521 r_work=0.1110 r_free=0.1521 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1110 r_free = 0.1521 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1105 r_free = 0.1520 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1105 r_free= 0.1520 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.935422 | | target function (ml) not normalized (work): 80116.698756 | | target function (ml) not normalized (free): 4162.799495 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1117 0.1392 5.462 5.6397| | 2: 3.63 - 2.88 1.00 2711 122 0.1078 0.1538 5.2169 5.383| | 3: 2.88 - 2.52 1.00 2681 148 0.1363 0.1704 5.1296 5.2138| | 4: 2.52 - 2.29 1.00 2661 139 0.0936 0.1452 4.6265 4.9095| | 5: 2.29 - 2.13 1.00 2678 122 0.0962 0.1489 4.577 4.8779| | 6: 2.13 - 2.00 1.00 2692 117 0.1121 0.1786 4.5709 4.7882| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.02 1.00 0.95 6330.85| | 2: 3.63 - 2.88 2711 122 0.92 12.78 1.01 0.95 6330.85| | 3: 2.88 - 2.52 2681 148 0.88 18.91 0.99 0.95 6330.85| | 4: 2.52 - 2.29 2661 139 0.93 12.07 1.01 0.97 2098.92| | 5: 2.29 - 2.13 2678 122 0.91 14.15 1.00 0.97 2098.92| | 6: 2.13 - 2.00 2692 117 0.89 16.77 0.99 0.97 2098.92| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2098.92 max = 6330.85 mean = 4237.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.93 mean = 13.91| |phase err.(test): min = 0.00 max = 86.10 mean = 13.37| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1105 0.1520 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1572 0.1563 0.1780 n_refl.: 17040 remove outliers: r(all,work,free)=0.1572 0.1563 0.1780 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1556 0.1547 0.1772 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1107 0.1517 n_refl.: 17040 remove outliers: r(all,work,free)=0.1127 0.1107 0.1517 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 0.3539 296.603 275.885 0.554 1.002 0.340 11.894-9.307 99.02 97 4 0.1761 487.855 481.310 0.913 1.003 0.340 9.237-7.194 100.00 213 7 0.1781 399.016 401.090 0.993 1.003 0.230 7.162-5.571 100.00 427 22 0.1568 299.462 293.975 0.938 1.003 0.204 5.546-4.326 100.00 867 58 0.0921 411.114 407.985 0.965 1.003 0.182 4.315-3.360 100.00 1859 96 0.0876 390.973 389.255 1.006 1.002 0.164 3.356-2.611 100.00 3867 181 0.1231 256.847 254.531 1.002 1.001 0.111 2.608-2.000 99.99 8818 434 0.1040 167.420 165.997 0.995 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8854 ================= 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 : 0.2782 0.1788 0.084 5.376 8.8 119.3 19.9 258 0.000 1_bss: 0.1612 0.1623 0.084 5.376 8.4 118.9 19.5 258 0.000 1_settarget: 0.1612 0.1623 0.084 5.376 8.4 118.9 19.5 258 0.000 1_nqh: 0.1614 0.1623 0.084 5.376 8.4 118.9 19.5 258 0.003 1_weight: 0.1614 0.1623 0.084 5.376 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1349 0.1639 0.009 0.964 8.4 118.9 19.5 258 0.155 1_adp: 0.1275 0.1663 0.009 0.964 6.5 113.9 20.0 258 0.155 1_regHadp: 0.1278 0.1670 0.009 0.964 6.5 113.9 20.0 258 0.155 1_occ: 0.1273 0.1664 0.009 0.964 6.5 113.9 20.0 258 0.155 2_bss: 0.1270 0.1657 0.009 0.964 6.2 113.5 19.6 258 0.155 2_settarget: 0.1270 0.1657 0.009 0.964 6.2 113.5 19.6 258 0.155 2_updatecdl: 0.1270 0.1657 0.009 0.982 6.2 113.5 19.6 258 0.155 2_nqh: 0.1272 0.1657 0.009 0.982 6.2 113.5 19.6 258 0.152 2_sol: 0.1230 0.1556 0.009 0.982 6.2 112.1 21.0 363 n/a 2_weight: 0.1230 0.1556 0.009 0.982 6.2 112.1 21.0 363 n/a 2_xyzrec: 0.1202 0.1593 0.008 0.925 6.2 112.1 21.0 363 n/a 2_adp: 0.1190 0.1608 0.008 0.925 6.8 107.1 21.5 363 n/a 2_regHadp: 0.1192 0.1609 0.008 0.925 6.8 107.1 21.5 363 n/a 2_occ: 0.1190 0.1610 0.008 0.925 6.8 107.1 21.5 363 n/a 3_bss: 0.1186 0.1603 0.008 0.925 6.4 106.7 21.2 363 n/a 3_settarget: 0.1186 0.1603 0.008 0.925 6.4 106.7 21.2 363 n/a 3_updatecdl: 0.1186 0.1603 0.008 0.930 6.4 106.7 21.2 363 n/a 3_nqh: 0.1186 0.1603 0.008 0.930 6.4 106.7 21.2 363 n/a 3_sol: 0.1198 0.1527 0.008 0.930 6.4 106.7 21.2 401 n/a 3_weight: 0.1198 0.1527 0.008 0.930 6.4 106.7 21.2 401 n/a 3_xyzrec: 0.1176 0.1535 0.009 0.954 6.4 106.7 21.2 401 n/a 3_adp: 0.1155 0.1553 0.009 0.954 6.6 104.3 21.0 401 n/a 3_regHadp: 0.1155 0.1553 0.009 0.954 6.6 104.3 21.0 401 n/a 3_occ: 0.1145 0.1546 0.009 0.954 6.6 104.3 21.0 401 n/a 4_bss: 0.1142 0.1545 0.009 0.954 6.2 103.9 20.6 401 n/a 4_settarget: 0.1142 0.1545 0.009 0.954 6.2 103.9 20.6 401 n/a 4_updatecdl: 0.1142 0.1545 0.009 0.953 6.2 103.9 20.6 401 n/a 4_nqh: 0.1142 0.1545 0.009 0.953 6.2 103.9 20.6 401 n/a 4_sol: 0.1121 0.1512 0.009 0.953 6.2 103.9 21.1 448 n/a 4_weight: 0.1121 0.1512 0.009 0.953 6.2 103.9 21.1 448 n/a 4_xyzrec: 0.1111 0.1554 0.009 0.969 6.2 103.9 21.1 448 n/a 4_adp: 0.1101 0.1554 0.009 0.969 6.2 102.1 21.1 448 n/a 4_regHadp: 0.1101 0.1554 0.009 0.969 6.2 102.1 21.1 448 n/a 4_occ: 0.1093 0.1547 0.009 0.969 6.2 102.1 21.1 448 n/a 5_bss: 0.1089 0.1542 0.009 0.969 5.9 101.8 20.8 448 n/a 5_settarget: 0.1089 0.1542 0.009 0.969 5.9 101.8 20.8 448 n/a 5_updatecdl: 0.1089 0.1542 0.009 0.971 5.9 101.8 20.8 448 n/a 5_setrh: 0.1091 0.1541 0.009 0.971 5.9 101.8 20.8 448 n/a 5_nqh: 0.1091 0.1541 0.009 0.971 5.9 101.8 20.8 448 n/a 5_sol: 0.1102 0.1501 0.009 0.971 5.9 101.8 20.8 450 n/a 5_weight: 0.1102 0.1501 0.009 0.971 5.9 101.8 20.8 450 n/a 5_xyzrec: 0.1118 0.1522 0.009 1.032 5.9 101.8 20.8 450 n/a 5_adp: 0.1110 0.1521 0.009 1.032 5.6 101.2 20.9 450 n/a 5_regHadp: 0.1110 0.1521 0.009 1.032 5.6 101.2 20.9 450 n/a 5_occ: 0.1105 0.1520 0.009 1.032 5.6 101.2 20.9 450 n/a end: 0.1107 0.1517 0.009 1.032 5.4 100.9 20.6 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9255201_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9255201_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3800 Refinement macro-cycles (run) : 918.3200 Write final files (write_after_run_outputs) : 20.5100 Total : 942.2100 Total CPU time: 16.08 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:05 PST -0800 (1735494065.59 s) Start R-work = 0.1612, R-free = 0.1623 Final R-work = 0.1107, R-free = 0.1517 =============================================================================== Job complete usr+sys time: 988.57 seconds wall clock time: 16 minutes 51.09 seconds (1011.09 seconds total)