Starting phenix.refine on Mon May 20 17:17:05 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4xcr.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4xcr/4xcr.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=True secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4xcr/4xcr.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4xcr/4xcr.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4xcr.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4xcr.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1543 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1543 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Time building chain proxies: 1.11, per 1000 atoms: 0.36 Number of scatterers: 3086 At special positions: 0 Unit cell: (70.8199, 70.8199, 70.01, 90, 90, 120) Space group: P 65 (No. 170) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 308 8.00 N 280 7.00 C 954 6.00 H 1544 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 - 3.50 Amino acid : False - 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: 1.49 Conformation dependent library (CDL) restraints added in 288.3 milliseconds 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 360 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.10: 1544 1.10 - 1.21: 0 1.21 - 1.33: 308 1.33 - 1.44: 336 1.44 - 1.56: 918 Bond restraints: 3106 Sorted by residual: bond pdb=" N GLY A 104 " pdb=" H GLY A 104 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA A 93 " pdb=" H ALA A 93 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS B 48 " pdb=" H HIS B 48 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLY A 10 " pdb=" H GLY A 10 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N SER B 103 " pdb=" H SER B 103 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 3101 not shown) Histogram of bond angle deviations from ideal: 102.64 - 108.90: 1201 108.90 - 115.16: 2931 115.16 - 121.42: 737 121.42 - 127.67: 747 127.67 - 133.93: 16 Bond angle restraints: 5632 Sorted by residual: angle pdb=" N HIS A 46 " pdb=" CA HIS A 46 " pdb=" C HIS A 46 " ideal model delta sigma weight residual 108.79 114.62 -5.83 1.53e+00 4.27e-01 1.45e+01 angle pdb=" N ALA B 50 " pdb=" CA ALA B 50 " pdb=" C ALA B 50 " ideal model delta sigma weight residual 108.13 114.63 -6.50 1.72e+00 3.38e-01 1.43e+01 angle pdb=" N HIS B 46 " pdb=" CA HIS B 46 " pdb=" C HIS B 46 " ideal model delta sigma weight residual 109.07 115.09 -6.02 1.61e+00 3.86e-01 1.40e+01 angle pdb=" N THR A 86 " pdb=" CA THR A 86 " pdb=" C THR A 86 " ideal model delta sigma weight residual 108.96 114.59 -5.63 1.59e+00 3.96e-01 1.26e+01 angle pdb=" N ALA A 109 " pdb=" CA ALA A 109 " pdb=" C ALA A 109 " ideal model delta sigma weight residual 112.93 108.80 4.13 1.33e+00 5.65e-01 9.65e+00 ... (remaining 5627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1281 17.29 - 34.57: 82 34.57 - 51.86: 49 51.86 - 69.15: 16 69.15 - 86.44: 2 Dihedral angle restraints: 1430 sinusoidal: 788 harmonic: 642 Sorted by residual: dihedral pdb=" CA HIS B 46 " pdb=" C HIS B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU B 101 " pdb=" C LEU B 101 " pdb=" N ALA B 102 " pdb=" CA ALA B 102 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE B 69 " pdb=" C ILE B 69 " pdb=" N GLU B 70 " pdb=" CA GLU B 70 " ideal model delta harmonic sigma weight residual 180.00 163.32 16.68 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 1427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 152 0.034 - 0.067: 46 0.067 - 0.101: 23 0.101 - 0.135: 17 0.135 - 0.168: 6 Chirality restraints: 244 Sorted by residual: chirality pdb=" CA VAL B 47 " pdb=" N VAL B 47 " pdb=" C VAL B 47 " pdb=" CB VAL B 47 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ILE A 18 " pdb=" N ILE A 18 " pdb=" C ILE A 18 " pdb=" CB ILE A 18 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE B 18 " pdb=" N ILE B 18 " pdb=" C ILE B 18 " pdb=" CB ILE B 18 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 241 not shown) Planarity restraints: 494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " -0.000 2.00e-02 2.50e+03 4.94e-03 7.31e-01 pdb=" CG PHE B 20 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 20 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE B 20 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE B 20 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 45 " 0.004 2.00e-02 2.50e+03 4.84e-03 7.02e-01 pdb=" CG PHE A 45 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 45 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 45 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 45 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 45 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 45 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 20 " 0.003 2.00e-02 2.50e+03 3.91e-03 4.58e-01 pdb=" CG PHE A 20 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 20 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 20 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 20 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHE A 20 " -0.001 2.00e-02 2.50e+03 ... (remaining 491 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.08: 168 2.08 - 2.69: 4385 2.69 - 3.29: 8530 3.29 - 3.90: 10967 3.90 - 4.50: 16312 Nonbonded interactions: 40362 Sorted by model distance: nonbonded pdb=" H GLY A 96 " pdb="HD21 ASN B 26 " model vdw sym.op. 1.477 2.100 -x+1,-y+1,z+1/2 nonbonded pdb=" O ALA B 4 " pdb=" H PHE B 20 " model vdw 1.502 1.850 nonbonded pdb=" OE2 GLU A 21 " pdb=" HE1 TRP A 32 " model vdw 1.545 1.850 nonbonded pdb=" O LEU B 42 " pdb=" H GLY B 94 " model vdw 1.609 1.850 nonbonded pdb=" H VAL A 47 " pdb=" O GLY A 52 " model vdw 1.623 1.850 ... (remaining 40357 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: 4 Type Number sf(0) Gaussians O 308 7.97 1 N 280 6.97 1 C 954 5.97 1 H 1544 1.00 1 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 ===================== Setting occupancies to: 1.000: selected atoms: 1544 of 3086 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3086 n_use_u_iso = 1544 n_use_u_aniso = 1542 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 = 3086 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3086 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1544 aniso = 1542) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 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 } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "4xcr_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1544 occupancy sum: 1544.00 (% of total atoms 50.09) Rotatable: count: 506 occupancy sum: 506.00 (% of total atoms 16.41) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.60 - 46.13 A, n_refl.=2197 (all), 9.97 % free)-------------| | | | r_work= 0.4859 r_free= 0.4533 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 6.422387 | | target function (ml) not normalized (work): 12703.482032 | | target function (ml) not normalized (free): 1443.643012 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 46.13 - 4.54 0.92 985 109 0.4372 0.4517 6.651 6.749| | 2: 4.53 - 3.60 0.94 993 110 0.5457 0.4551 6.1956 6.4364| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 46.13 - 4.54 985 109 0.66 38.01 0.84 0.99 177349.34| | 2: 4.53 - 3.60 993 110 0.87 20.59 2.01 1.79 35225.25| |alpha: min = 0.37 max = 2.03 mean = 1.39| |beta: min = 27468.29 max = 448438.04 mean = 105999.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 90.00 mean = 29.26| |phase err.(test): min = 0.00 max = 89.63 mean = 29.40| |-----------------------------------------------------------------------------| ----------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 : 0.005 0.024 1562 Z= 0.320 Angle : 1.074 6.499 2110 Z= 0.704 Chirality : 0.052 0.168 244 Planarity : 0.002 0.012 280 Dihedral : 14.220 86.435 540 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.33 % Favored : 90.74 % Rotamer: Outliers : 3.85 % Allowed : 7.69 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.86 (0.40), residues: 216 helix: None (None), residues: 0 sheet: -2.78 (0.43), residues: 94 loop : -3.71 (0.33), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 100 PHE 0.009 0.003 PHE A 45 TRP 0.004 0.001 TRP B 32 HIS 0.002 0.001 HIS B 80 Individual atomic B min max mean iso aniso Overall: 42.38 96.62 61.74 1.86 1542 0 Protein: 42.38 96.62 61.74 1.86 1542 0 Chain A: 42.38 92.35 59.13 N/A 771 0 Chain B: 46.95 96.62 64.36 N/A 771 0 Histogram: Values Number of atoms 42.38 - 47.80 75 47.80 - 53.23 307 53.23 - 58.65 306 58.65 - 64.08 257 64.08 - 69.50 241 69.50 - 74.92 185 74.92 - 80.35 96 80.35 - 85.77 43 85.77 - 91.20 25 91.20 - 96.62 7 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2197 (all), 9.97 % free)-------------| | | | r_work= 0.4859 r_free= 0.4533 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 6.422387 | | target function (ml) not normalized (work): 12703.482032 | | target function (ml) not normalized (free): 1443.643012 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3070 percent. r_work = 0.4990 r_free = 0.4731 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4964 0.4990 0.4731 n_refl.: 2197 re-set all scales: r(all,work,free)=0.4964 0.4990 0.4731 n_refl.: 2197 remove outliers: r(all,work,free)=0.4926 0.4948 0.4731 n_refl.: 2192 overall B=-12.88 to atoms: r(all,work,free)=0.4430 0.4444 0.4361 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2094 0.2035 0.2627 n_refl.: 2192 remove outliers: r(all,work,free)=0.2094 0.2035 0.2627 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.1851 812.492 781.541 1.249 1.028 0.367 10.083-8.012 89.47 92 10 0.2086 541.003 524.203 1.179 1.018 0.365 8.010-6.369 94.31 180 19 0.2300 513.402 486.339 1.059 1.011 0.363 6.360-5.059 92.00 354 37 0.1977 502.797 476.188 0.934 1.003 0.366 5.057-4.020 93.59 707 82 0.1974 525.069 501.856 0.990 0.990 0.283 4.017-3.602 94.20 556 61 0.2122 381.422 353.384 1.010 0.980 0.255 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.8283 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.571823 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.265339 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2139 0.2776 0.0637 0.002 0.4 1.9 0.0 4.5 0 0.125 0.2092 0.2779 0.0687 0.002 0.4 2.9 0.0 4.5 0 0.250 0.2016 0.2775 0.0759 0.002 0.5 2.9 0.0 4.5 0 0.500 0.1910 0.2809 0.0900 0.003 0.6 3.6 0.0 4.5 0 1.000 0.1841 0.2870 0.1028 0.005 0.7 4.5 0.0 5.8 0 2.000 0.1800 0.2909 0.1109 0.007 0.8 6.8 0.0 5.8 0 3.000 0.1756 0.2919 0.1163 0.008 0.9 8.4 0.0 6.4 0 4.000 0.1719 0.2912 0.1193 0.010 1.0 9.7 0.0 7.7 0 5.000 0.1699 0.2922 0.1223 0.011 1.1 11.3 0.0 8.3 0 6.000 0.1672 0.2982 0.1310 0.012 1.2 13.6 0.0 9.6 0 7.000 0.1664 0.2926 0.1262 0.013 1.3 13.9 0.0 9.6 0 8.000 0.1642 0.2930 0.1288 0.014 1.4 15.9 0.5 9.6 0 9.000 0.1636 0.2949 0.1312 0.015 1.4 15.9 0.5 10.9 0 10.000 0.1684 0.2948 0.1264 0.012 1.2 13.0 0.0 9.6 0 6.786 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2016 0.2775 0.0759 0.002 0.5 2.9 0.0 4.5 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.16 27.75 7.59 8.919 45.386 0.265 0.053 20.41 28.35 7.94 8.125 45.901 0.008 0.054 19.47 28.01 8.54 8.570 45.658 0.033 0.050 18.87 27.68 8.81 9.190 45.506 0.133 0.047 18.20 27.56 9.36 9.856 45.725 0.265 0.044 17.09 27.29 10.20 11.999 46.515 0.398 0.039 16.88 27.25 10.38 12.620 46.746 0.531 0.038 16.74 27.25 10.51 13.076 46.916 0.663 0.037 16.54 27.24 10.70 13.674 47.171 0.796 0.036 16.20 27.28 11.08 14.750 47.654 0.929 0.035 15.99 27.35 11.36 15.543 47.990 1.061 0.034 15.89 27.37 11.48 15.913 48.129 1.194 0.034 15.80 27.42 11.62 16.335 48.295 1.327 0.033 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.008 Accepted refinement result: 20.41 28.35 7.94 8.125 45.901 0.008 0.054 Individual atomic B min max mean iso aniso Overall: 35.35 78.74 49.90 1.33 1542 0 Protein: 35.35 78.74 49.90 1.33 1542 0 Chain A: 35.35 74.47 47.66 N/A 771 0 Chain B: 37.04 78.74 52.14 N/A 771 0 Histogram: Values Number of atoms 35.35 - 39.69 185 39.69 - 44.03 272 44.03 - 48.37 224 48.37 - 52.71 278 52.71 - 57.05 299 57.05 - 61.39 145 61.39 - 65.73 86 65.73 - 70.07 25 70.07 - 74.40 18 74.40 - 78.74 10 =========================== Idealize ADP of riding H ========================== r_work=0.2041 r_free=0.2835 r_work=0.2038 r_free=0.2807 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.2038 r_free= 0.2807 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.054291 | | target function (ls_wunit_k1) not normalized (work): 107.115598 | | target function (ls_wunit_k1) not normalized (free): 22.738753 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2113 0.2038 0.2807 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4460 0.4464 0.4494 n_refl.: 2192 remove outliers: r(all,work,free)=0.4460 0.4464 0.4494 n_refl.: 2192 overall B=1.55 to atoms: r(all,work,free)=0.4518 0.4523 0.4531 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2094 0.2022 0.2748 n_refl.: 2192 remove outliers: r(all,work,free)=0.2094 0.2022 0.2748 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.1745 485.733 474.378 1.173 1.124 0.372 10.083-8.012 89.47 92 10 0.1899 323.429 316.288 1.120 1.095 0.374 8.010-6.369 93.43 180 19 0.2212 306.928 298.451 1.027 1.067 0.377 6.360-5.059 92.00 354 37 0.1962 300.588 286.828 0.933 1.029 0.375 5.057-4.020 93.48 707 82 0.1993 313.903 299.520 1.029 0.966 0.275 4.017-3.602 94.20 556 61 0.2153 228.026 209.389 1.094 0.908 0.263 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.9606 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.020806 wxc_scale = 0.038 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.040697 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2205 0.2845 0.0640 0.001 0.4 2.3 0.0 3.2 0 0.008 0.2127 0.2801 0.0674 0.001 0.4 2.6 0.0 3.2 0 0.023 0.2042 0.2788 0.0746 0.002 0.4 2.9 0.0 3.8 0 0.046 0.1980 0.2787 0.0807 0.002 0.5 2.9 0.0 3.8 0 0.068 0.1945 0.2808 0.0863 0.002 0.5 2.9 0.0 3.8 0 0.091 0.1920 0.2818 0.0898 0.003 0.5 3.6 0.0 3.8 0 0.114 0.1900 0.2827 0.0927 0.003 0.5 3.2 0.0 3.8 0 0.137 0.1894 0.2880 0.0985 0.003 0.6 3.9 0.0 3.8 0 0.160 0.1961 0.2790 0.0830 0.002 0.5 3.2 0.0 3.8 0 0.076 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2042 0.2788 0.0746 0.002 0.4 2.9 0.0 3.8 0 0.046 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.42 27.88 7.46 7.149 56.219 0.041 5.646 20.94 28.47 7.53 7.253 57.550 0.001 5.666 19.12 27.53 8.41 7.110 57.731 0.005 5.582 17.58 27.36 9.78 8.680 57.267 0.020 5.498 17.24 27.46 10.22 9.424 57.421 0.041 5.477 16.93 27.45 10.52 10.240 57.758 0.061 5.457 16.88 27.54 10.66 10.482 57.811 0.081 5.453 16.75 27.55 10.79 10.941 57.991 0.102 5.445 16.47 27.47 10.99 12.002 58.416 0.122 5.427 16.39 27.49 11.10 12.412 58.558 0.142 5.422 16.33 27.50 11.17 12.748 58.674 0.163 5.418 16.27 27.50 11.22 13.110 58.794 0.183 5.413 16.25 27.51 11.26 13.279 58.852 0.203 5.411 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 19.12 27.53 8.41 7.110 57.731 0.005 5.582 Individual atomic B min max mean iso aniso Overall: 32.40 85.75 54.47 2.42 1542 0 Protein: 32.40 85.75 54.47 2.42 1542 0 Chain A: 32.40 85.75 52.07 N/A 771 0 Chain B: 34.36 84.09 56.88 N/A 771 0 Histogram: Values Number of atoms 32.40 - 37.74 83 37.74 - 43.07 138 43.07 - 48.41 243 48.41 - 53.74 301 53.74 - 59.07 252 59.07 - 64.41 259 64.41 - 69.74 151 69.74 - 75.08 67 75.08 - 80.41 38 80.41 - 85.75 10 =========================== Idealize ADP of riding H ========================== r_work=0.1912 r_free=0.2753 r_work=0.1907 r_free=0.2755 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.1907 r_free= 0.2755 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 5.580140 | | target function (ml) not normalized (work): 11009.615579 | | target function (ml) not normalized (free): 1334.405068 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1991 0.1907 0.2755 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4590 0.4595 0.4594 n_refl.: 2192 remove outliers: r(all,work,free)=0.4590 0.4595 0.4594 n_refl.: 2192 overall B=0.00 to atoms: r(all,work,free)=0.4590 0.4595 0.4594 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.1995 0.1907 0.2804 n_refl.: 2192 remove outliers: r(all,work,free)=0.1995 0.1907 0.2804 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.1829 485.733 472.772 1.110 1.095 0.361 10.083-8.012 89.47 92 10 0.1985 323.429 315.654 1.077 1.069 0.362 8.010-6.369 93.43 180 19 0.2195 306.928 295.573 1.011 1.047 0.362 6.360-5.059 92.00 354 37 0.1882 300.588 287.050 0.913 1.018 0.350 5.057-4.020 93.48 707 82 0.1867 313.903 300.466 1.022 0.969 0.260 4.017-3.602 94.20 556 61 0.1874 228.026 212.226 1.081 0.925 0.230 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=2.2874 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 432 Ramachandran restraints generated. 216 Oldfield, 0 Emsley, 216 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1907 r_free=0.2804 After: r_work=0.1907 r_free=0.2804 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.805105 wxc_scale = 0.034 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.036754 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1915 0.2806 0.0891 0.002 0.4 2.9 0.0 3.8 0 0.006 0.1912 0.2805 0.0893 0.002 0.4 2.6 0.0 3.8 0 0.019 0.1909 0.2804 0.0895 0.002 0.4 2.6 0.0 3.8 0 0.037 0.1907 0.2805 0.0898 0.002 0.4 2.9 0.0 3.8 0 0.056 0.1905 0.2806 0.0901 0.002 0.4 2.9 0.0 3.8 0 0.074 0.1901 0.2804 0.0903 0.002 0.5 2.6 0.0 3.8 0 0.093 0.1896 0.2799 0.0904 0.003 0.5 2.6 0.0 3.8 0 0.111 0.1892 0.2797 0.0905 0.003 0.5 2.9 0.0 3.8 0 0.130 0.1906 0.2805 0.0899 0.002 0.4 2.6 0.0 3.8 0 0.062 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1892 0.2797 0.0905 0.003 0.5 2.9 0.0 3.8 0 0.130 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.92 27.97 9.05 7.941 59.649 0.037 5.574 20.38 28.61 8.24 8.200 61.161 0.001 5.638 19.30 28.11 8.81 7.981 60.866 0.005 5.590 16.81 27.64 10.83 9.132 60.539 0.018 5.452 16.37 27.73 11.37 10.019 60.710 0.037 5.422 16.13 27.74 11.61 10.714 60.965 0.055 5.405 15.96 27.74 11.77 11.255 61.169 0.074 5.394 15.83 27.74 11.91 11.784 61.376 0.092 5.385 15.73 27.75 12.02 12.206 61.535 0.110 5.379 15.64 27.74 12.10 12.606 61.680 0.129 5.373 15.58 27.76 12.18 12.902 61.786 0.147 5.369 15.52 27.77 12.25 13.254 61.909 0.165 5.365 15.50 27.78 12.28 13.409 61.964 0.184 5.363 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 19.30 28.11 8.81 7.981 60.866 0.005 5.590 Individual atomic B min max mean iso aniso Overall: 37.49 84.78 56.91 2.27 1542 0 Protein: 37.49 84.78 56.91 2.27 1542 0 Chain A: 37.49 80.75 54.86 N/A 771 0 Chain B: 39.79 84.78 58.95 N/A 771 0 Histogram: Values Number of atoms 37.49 - 42.21 26 42.21 - 46.94 200 46.94 - 51.67 268 51.67 - 56.40 279 56.40 - 61.13 288 61.13 - 65.86 223 65.86 - 70.59 157 70.59 - 75.32 58 75.32 - 80.05 22 80.05 - 84.78 21 =========================== Idealize ADP of riding H ========================== r_work=0.1930 r_free=0.2811 r_work=0.1933 r_free=0.2806 ----------X-ray data---------- |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.1933 r_free= 0.2806 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 5.591591 | | target function (ml) not normalized (work): 11032.208917 | | target function (ml) not normalized (free): 1337.354797 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 46.13 - 4.54 0.92 980 109 0.1933 0.2883 5.7041 6.1618| | 2: 4.53 - 3.60 0.94 993 110 0.1933 0.2717 5.4806 6.052| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 46.13 - 4.54 980 109 0.89 17.64 0.99 1.05 13593.11| | 2: 4.53 - 3.60 993 110 0.92 15.28 1.02 1.07 7697.37| |alpha: min = 1.01 max = 1.12 mean = 1.06| |beta: min = 5253.80 max = 18836.43 mean = 10625.82| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 90.00 mean = 16.45| |phase err.(test): min = 0.00 max = 85.77 mean = 16.34| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2020 0.1933 0.2806 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4711 0.4718 0.4710 n_refl.: 2192 remove outliers: r(all,work,free)=0.4711 0.4718 0.4710 n_refl.: 2192 overall B=-0.16 to atoms: r(all,work,free)=0.4705 0.4711 0.4706 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2015 0.1930 0.2791 n_refl.: 2192 remove outliers: r(all,work,free)=0.2015 0.1930 0.2791 n_refl.: 2192 ======================== 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 46.133-10.115 85.45 84 10 0.1834 485.733 466.840 1.149 1.069 0.370 10.083-8.012 89.47 92 10 0.1983 323.429 312.874 1.085 1.049 0.367 8.010-6.369 93.43 180 19 0.2164 306.928 293.381 1.009 1.033 0.364 6.360-5.059 92.00 354 37 0.1955 300.588 284.882 0.915 1.011 0.350 5.057-4.020 93.48 707 82 0.1899 313.903 301.664 1.029 0.977 0.271 4.017-3.602 94.20 556 61 0.1880 228.026 214.214 1.085 0.946 0.241 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.4551 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4859 0.4533 0.005 1.074 42.4 96.6 61.7 0 0.000 1_bss: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_settarget: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_updatephipsi: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_weight: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_xyzrec: 0.2016 0.2775 0.002 0.478 29.5 83.7 48.9 0 0.150 1_adp: 0.2041 0.2835 0.002 0.478 35.4 78.7 49.9 0 0.150 1_regHadp: 0.2038 0.2807 0.002 0.478 35.4 78.7 49.9 0 0.150 2_bss: 0.2022 0.2748 0.002 0.478 36.9 80.3 51.4 0 0.150 2_settarget: 0.2022 0.2748 0.002 0.478 36.9 80.3 51.4 0 0.150 2_updatephipsi: 0.2022 0.2748 0.002 0.478 36.9 80.3 51.4 0 0.150 2_updatecdl: 0.2022 0.2748 0.002 0.511 36.9 80.3 51.4 0 0.150 2_weight: 0.2022 0.2748 0.002 0.511 36.9 80.3 51.4 0 0.150 2_xyzrec: 0.2042 0.2788 0.002 0.422 36.9 80.3 51.4 0 0.188 2_adp: 0.1912 0.2753 0.002 0.422 32.4 85.7 54.5 0 0.188 2_regHadp: 0.1907 0.2755 0.002 0.422 32.4 85.7 54.5 0 0.188 3_bss: 0.1907 0.2804 0.002 0.422 32.4 85.7 54.5 0 0.188 3_settarget: 0.1907 0.2804 0.002 0.422 32.4 85.7 54.5 0 0.188 3_updatephipsi: 0.1907 0.2804 0.002 0.422 32.4 85.7 54.5 0 0.188 3_updatecdl: 0.1907 0.2804 0.002 0.467 32.4 85.7 54.5 0 0.188 3_setrh: 0.1907 0.2804 0.002 0.467 32.4 85.7 54.5 0 0.188 3_weight: 0.1907 0.2804 0.002 0.467 32.4 85.7 54.5 0 0.188 3_xyzrec: 0.1892 0.2797 0.003 0.467 32.4 85.7 54.5 0 0.189 3_adp: 0.1930 0.2811 0.003 0.467 37.5 84.8 56.9 0 0.189 3_regHadp: 0.1933 0.2806 0.003 0.467 37.5 84.8 56.9 0 0.189 end: 0.1930 0.2791 0.003 0.467 37.3 84.6 56.7 0 0.189 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/4xcr_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/4xcr_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.4400 Refinement macro-cycles (run) : 104.7600 Write final files (write_after_run_outputs) : 13.2300 Total : 122.4300 Total CPU time: 2.46 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:25:39 PDT -0700 (1716251139.57 s) Start R-work = 0.2035, R-free = 0.2627 Final R-work = 0.1930, R-free = 0.2791 =============================================================================== Job complete usr+sys time: 155.65 seconds wall clock time: 8 minutes 56.60 seconds (536.60 seconds total)