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/1m10.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1m10.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1m10.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1m10/1m10.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 } 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 Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 7468 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3250 Classifications: {'peptide': 199} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "B" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 4218 Classifications: {'peptide': 267} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 246} Time building chain proxies: 2.37, per 1000 atoms: 0.32 Number of scatterers: 7468 At special positions: 0 Unit cell: (89.84, 89.84, 124.63, 90, 90, 120) Space group: P 61 (No. 169) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 682 8.00 N 628 7.00 C 2366 6.00 H 3778 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 695 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 17 " distance=2.03 Simple disulfide: pdb=" SG CYS B 209 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 211 " - pdb=" SG CYS B 264 " distance=2.04 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: 4.31 Conformation dependent library (CDL) restraints added in 590.7 milliseconds 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 886 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3777 1.15 - 1.32: 698 1.32 - 1.49: 1420 1.49 - 1.67: 1630 1.67 - 1.84: 19 Bond restraints: 7544 Sorted by residual: bond pdb=" N VAL B 256 " pdb=" H VAL B 256 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLU A 700 " pdb=" H GLU A 700 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N SER B 114 " pdb=" H SER B 114 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND1 HIS A 563 " pdb=" HD1 HIS A 563 " 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 195 " pdb=" H HIS B 195 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7539 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.21: 392 106.21 - 113.18: 8799 113.18 - 120.15: 2310 120.15 - 127.12: 2204 127.12 - 134.09: 31 Bond angle restraints: 13736 Sorted by residual: angle pdb=" N VAL B 78 " pdb=" CA VAL B 78 " pdb=" C VAL B 78 " ideal model delta sigma weight residual 112.43 120.71 -8.28 9.20e-01 1.18e+00 8.10e+01 angle pdb=" C LEU B 76 " pdb=" N PRO B 77 " pdb=" CA PRO B 77 " ideal model delta sigma weight residual 119.84 130.41 -10.57 1.25e+00 6.40e-01 7.15e+01 angle pdb=" C LEU B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.56 127.99 -8.43 1.02e+00 9.61e-01 6.83e+01 angle pdb=" N ILE B 213 " pdb=" CA ILE B 213 " pdb=" C ILE B 213 " ideal model delta sigma weight residual 112.90 105.33 7.57 9.60e-01 1.09e+00 6.21e+01 angle pdb=" N ARG A 511 " pdb=" CA ARG A 511 " pdb=" C ARG A 511 " ideal model delta sigma weight residual 108.45 118.26 -9.81 1.26e+00 6.30e-01 6.06e+01 ... (remaining 13731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3167 17.57 - 35.14: 236 35.14 - 52.71: 102 52.71 - 70.28: 32 70.28 - 87.84: 4 Dihedral angle restraints: 3541 sinusoidal: 1982 harmonic: 1559 Sorted by residual: dihedral pdb=" CA LYS A 585 " pdb=" CB LYS A 585 " pdb=" CG LYS A 585 " pdb=" CD LYS A 585 " ideal model delta sinusoidal sigma weight residual -60.00 -118.49 58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN B 159 " pdb=" CB GLN B 159 " pdb=" CG GLN B 159 " pdb=" CD GLN B 159 " ideal model delta sinusoidal sigma weight residual 60.00 113.33 -53.33 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" C HIS B 195 " pdb=" N HIS B 195 " pdb=" CA HIS B 195 " pdb=" CB HIS B 195 " ideal model delta harmonic sigma weight residual -122.60 -115.04 -7.56 0 2.50e+00 1.60e-01 9.15e+00 ... (remaining 3538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 349 0.080 - 0.160: 177 0.160 - 0.240: 54 0.240 - 0.320: 12 0.320 - 0.400: 4 Chirality restraints: 596 Sorted by residual: chirality pdb=" CA PRO B 2 " pdb=" N PRO B 2 " pdb=" C PRO B 2 " pdb=" CB PRO B 2 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA GLN B 21 " pdb=" N GLN B 21 " pdb=" C GLN B 21 " pdb=" CB GLN B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA HIS B 195 " pdb=" N HIS B 195 " pdb=" C HIS B 195 " pdb=" CB HIS B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 593 not shown) Planarity restraints: 1091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 44 " -0.125 2.00e-02 2.50e+03 5.17e-02 8.01e+01 pdb=" CG TYR B 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 44 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 44 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 44 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 44 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 44 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 44 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 TYR B 44 " 0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 44 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR B 44 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR B 44 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 600 " 0.122 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" CG TYR A 600 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 600 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 600 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 600 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 600 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 600 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 600 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 54 " 0.112 2.00e-02 2.50e+03 4.13e-02 5.13e+01 pdb=" CG TYR B 54 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 54 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 54 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 54 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 54 " 0.042 2.00e-02 2.50e+03 pdb=" HD1 TYR B 54 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR B 54 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR B 54 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 54 " 0.006 2.00e-02 2.50e+03 ... (remaining 1088 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 115 1.73 - 2.45: 4531 2.45 - 3.17: 24552 3.17 - 3.88: 32886 3.88 - 4.60: 50977 Nonbonded interactions: 113061 Sorted by model distance: nonbonded pdb=" HA HIS A 559 " pdb=" HA ALA A 592 " model vdw 1.014 2.440 nonbonded pdb="HH22 ARG A 545 " pdb=" HG3 PRO A 703 " model vdw 1.092 2.270 nonbonded pdb=" HA ARG A 636 " pdb="HH11 ARG A 636 " model vdw 1.130 2.270 nonbonded pdb="HD22 LEU A 512 " pdb="HH21 ARG A 611 " model vdw 1.155 2.270 nonbonded pdb=" OE1 GLU A 613 " pdb=" H GLU A 613 " model vdw 1.278 1.850 ... (remaining 113056 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: 5 Type Number sf(0) Gaussians S 14 15.96 2 O 682 7.97 1 N 628 6.97 1 C 2366 5.97 2 H 3778 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: 3778 of 7468 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7468 n_use_u_iso = 7468 n_use_u_aniso = 0 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 = 7468 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7468 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7468 aniso = 0) 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 = "1m10_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3778 occupancy sum: 3778.00 (% of total atoms 50.59) Rotatable: count: 1103 occupancy sum: 1103.00 (% of total atoms 14.77) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.09 - 30.50 A, n_refl.=10454 (all), 5.11 % free)------------| | | | r_work= 0.3804 r_free= 0.4305 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.437560 | | target function (ml) not normalized (work): 53940.591815 | | target function (ml) not normalized (free): 2943.016547 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 30.50 - 4.90 1.00 2530 123 0.3660 0.4501 6.0037 5.8545| | 2: 4.90 - 3.90 1.00 2453 134 0.3747 0.3971 5.604 5.8298| | 3: 3.89 - 3.40 1.00 2476 150 0.4079 0.4323 5.2694 5.4009| | 4: 3.40 - 3.09 1.00 2461 127 0.3903 0.4710 4.8588 4.973| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 30.50 - 4.90 2530 123 0.59 44.84 0.82 0.19 23753.52| | 2: 4.90 - 3.90 2453 134 0.66 39.62 1.40 0.30 15554.07| | 3: 3.89 - 3.40 2476 150 0.61 43.67 1.52 0.32 9054.65| | 4: 3.40 - 3.09 2461 127 0.53 49.92 1.29 0.25 4255.28| |alpha: min = 0.19 max = 0.32 mean = 0.27| |beta: min = 4255.28 max = 23753.52 mean = 13219.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.60| |phase err.(work): min = 0.00 max = 89.91 mean = 44.52| |phase err.(test): min = 0.00 max = 89.08 mean = 44.81| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.119 3766 Z= 0.622 Angle : 1.710 10.944 5117 Z= 1.081 Chirality : 0.104 0.400 596 Planarity : 0.010 0.086 656 Dihedral : 15.487 87.844 1425 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 35.50 Ramachandran Plot: Outliers : 4.98 % Allowed : 12.77 % Favored : 82.25 % Rotamer: Outliers : 5.28 % Allowed : 6.24 % Favored : 88.49 % 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: -5.24 (0.31), residues: 462 helix: -4.51 (0.29), residues: 98 sheet: -2.23 (0.51), residues: 89 loop : -3.68 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 545 TYR 0.104 0.022 TYR B 44 PHE 0.051 0.010 PHE B 201 TRP 0.058 0.016 TRP B 219 HIS 0.003 0.001 HIS B 86 Individual atomic B min max mean iso aniso Overall: 15.65 95.55 52.24 1.37 3690 0 Protein: 15.65 95.55 52.24 1.37 3690 0 Chain A: 21.62 95.55 60.64 N/A 1602 0 Chain B: 15.65 77.97 45.80 N/A 2088 0 Histogram: Values Number of atoms 15.65 - 23.64 14 23.64 - 31.63 190 31.63 - 39.62 520 39.62 - 47.61 817 47.61 - 55.60 852 55.60 - 63.59 530 63.59 - 71.58 302 71.58 - 79.57 236 79.57 - 87.56 164 87.56 - 95.55 65 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10454 (all), 5.11 % free)------------| | | | r_work= 0.3804 r_free= 0.4305 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.437560 | | target function (ml) not normalized (work): 53940.591815 | | target function (ml) not normalized (free): 2943.016547 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3828 0.3804 0.4305 n_refl.: 10454 re-set all scales: r(all,work,free)=0.3828 0.3804 0.4305 n_refl.: 10454 remove outliers: r(all,work,free)=0.3829 0.3805 0.4299 n_refl.: 10449 overall B=16.31 to atoms: r(all,work,free)=0.4448 0.4429 0.4826 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2288 0.2260 0.2819 n_refl.: 10449 remove outliers: r(all,work,free)=0.2288 0.2260 0.2819 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2311 1395.912 1343.970 1.051 1.212 0.395 14.512-11.594 100.00 95 5 0.1560 1328.531 1301.200 0.918 1.199 0.369 11.568-9.227 100.00 193 11 0.1404 1283.724 1248.849 0.929 1.180 0.359 9.162-7.352 100.00 368 15 0.2071 850.463 820.636 0.919 1.149 0.348 7.349-5.862 100.00 740 33 0.2226 628.811 611.546 0.853 1.103 0.326 5.858-4.671 100.00 1425 79 0.1948 673.689 650.894 0.916 1.028 0.283 4.669-3.723 99.86 2790 156 0.2269 618.917 593.677 1.202 0.910 0.181 3.723-3.092 99.93 4210 230 0.2720 337.947 316.886 1.511 0.750 0.063 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-5.7724 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.822367 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.201646 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.2377 0.2755 0.0378 0.003 0.6 5.0 0.4 3.6 0 0.125 0.2352 0.2744 0.0392 0.003 0.6 5.1 0.4 3.6 0 0.250 0.2309 0.2727 0.0418 0.003 0.6 4.6 0.4 3.6 0 0.500 0.2244 0.2694 0.0450 0.004 0.7 6.2 0.4 3.6 0 1.000 0.2182 0.2710 0.0528 0.005 0.8 7.4 0.6 4.3 0 2.000 0.2136 0.2715 0.0579 0.007 0.9 9.8 0.6 4.6 0 3.000 0.2104 0.2751 0.0647 0.008 1.0 11.8 0.9 5.0 0 4.000 0.2094 0.2721 0.0627 0.011 1.2 14.7 1.1 4.8 0 5.000 0.2074 0.2741 0.0668 0.012 1.3 15.5 1.3 5.0 0 6.000 0.2058 0.2740 0.0682 0.013 1.4 17.3 1.3 5.8 0 7.000 0.2042 0.2754 0.0712 0.014 1.4 18.0 1.5 6.0 0 8.000 0.2031 0.2749 0.0718 0.015 1.5 18.6 1.5 6.2 0 9.000 0.2019 0.2758 0.0739 0.016 1.6 19.2 1.7 7.0 0 10.000 0.2044 0.2754 0.0710 0.014 1.4 18.0 1.5 6.0 0 7.911 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2309 0.2727 0.0418 0.003 0.6 4.6 0.4 3.6 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.09 27.27 4.18 0.970 68.287 0.202 0.058 23.29 27.31 4.02 1.900 68.385 0.006 0.059 22.90 27.23 4.33 1.990 68.443 0.025 0.057 22.11 27.07 4.97 2.874 68.572 0.101 0.053 21.07 26.85 5.78 5.991 69.131 0.202 0.049 20.79 26.81 6.02 7.012 69.369 0.302 0.048 20.47 26.75 6.28 8.343 69.817 0.403 0.046 20.33 26.74 6.41 9.046 70.015 0.504 0.046 20.23 26.74 6.52 9.616 70.178 0.605 0.045 20.10 26.77 6.67 10.381 70.426 0.706 0.044 20.00 26.80 6.79 10.987 70.615 0.807 0.044 19.98 26.82 6.84 11.201 70.662 0.907 0.044 19.71 26.89 7.18 13.079 71.313 1.008 0.043 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.202 Accepted refinement result: 21.07 26.85 5.78 5.991 69.131 0.202 0.049 Individual atomic B min max mean iso aniso Overall: 36.09 120.35 70.26 5.94 3690 0 Protein: 36.09 120.35 70.26 5.94 3690 0 Chain A: 36.39 120.35 78.04 N/A 1602 0 Chain B: 36.09 117.31 64.30 N/A 2088 0 Histogram: Values Number of atoms 36.09 - 44.51 68 44.51 - 52.94 353 52.94 - 61.36 706 61.36 - 69.79 915 69.79 - 78.22 643 78.22 - 86.64 405 86.64 - 95.07 302 95.07 - 103.50 215 103.50 - 111.92 70 111.92 - 120.35 13 =========================== Idealize ADP of riding H ========================== r_work=0.2107 r_free=0.2685 r_work=0.2084 r_free=0.2670 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2084 r_free= 0.2670 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ls_wunit_k1) (work): 0.047684 | | target function (ls_wunit_k1) not normalized (work): 472.833278 | | target function (ls_wunit_k1) not normalized (free): 43.933637 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2114 0.2084 0.2670 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4381 0.4362 0.4758 n_refl.: 10449 remove outliers: r(all,work,free)=0.4381 0.4362 0.4758 n_refl.: 10449 overall B=-6.03 to atoms: r(all,work,free)=0.4136 0.4115 0.4539 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2127 0.2096 0.2711 n_refl.: 10449 remove outliers: r(all,work,free)=0.2127 0.2096 0.2711 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2189 771.893 751.902 1.348 1.123 0.402 14.512-11.594 100.00 95 5 0.1361 734.633 730.012 1.112 1.114 0.363 11.568-9.227 100.00 193 11 0.1387 709.856 698.412 1.123 1.103 0.365 9.162-7.352 100.00 368 15 0.1747 470.278 461.568 1.096 1.084 0.368 7.349-5.862 100.00 740 33 0.2001 347.711 342.149 0.971 1.056 0.342 5.858-4.671 100.00 1425 79 0.1834 372.528 363.171 0.977 1.011 0.296 4.669-3.723 99.93 2790 156 0.2022 342.240 333.979 1.173 0.940 0.197 3.723-3.092 100.00 4210 230 0.2650 186.873 177.582 1.315 0.844 0.057 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=-0.4641 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.528793 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.044053 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.2086 0.2670 0.0584 0.002 0.6 5.1 0.4 1.9 0 0.125 0.2041 0.2679 0.0638 0.003 0.6 6.3 0.4 3.1 0 0.250 0.2004 0.2701 0.0697 0.006 0.8 7.4 0.4 4.6 0 0.500 0.1958 0.2728 0.0769 0.009 1.0 10.3 0.4 5.0 0 1.000 0.1911 0.2746 0.0834 0.015 1.4 14.9 0.4 5.8 0 2.000 0.1889 0.2763 0.0874 0.020 1.7 17.5 0.9 6.2 0 3.000 0.1869 0.2765 0.0896 0.024 2.0 19.8 1.5 6.5 0 4.000 0.1846 0.2746 0.0900 0.028 2.2 21.7 1.3 6.7 0 5.000 0.1839 0.2724 0.0885 0.031 2.4 27.7 1.5 13.2 0 6.000 0.1822 0.2762 0.0941 0.035 2.7 24.9 1.7 7.4 0 7.000 0.1821 0.2744 0.0923 0.037 2.8 31.9 1.7 13.9 0 8.000 0.1812 0.2769 0.0956 0.040 3.1 34.8 1.7 15.6 0 9.000 0.1802 0.2772 0.0970 0.043 3.2 35.4 1.9 15.6 0 10.000 0.1922 0.2735 0.0814 0.013 1.3 14.2 0.4 5.8 0 1.764 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2086 0.2670 0.0584 0.002 0.6 5.1 0.4 1.9 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.86 26.70 5.84 11.016 71.417 0.044 5.749 23.95 28.46 4.50 8.992 75.353 0.001 5.814 23.24 27.74 4.50 10.897 73.324 0.006 5.798 20.96 26.62 5.67 11.215 71.171 0.022 5.743 20.73 26.62 5.89 11.416 71.122 0.044 5.738 20.53 26.57 6.03 11.852 70.947 0.066 5.731 19.98 26.54 6.56 13.576 71.548 0.088 5.709 20.05 26.49 6.44 13.057 71.089 0.110 5.712 19.98 26.51 6.53 13.179 71.197 0.132 5.711 19.93 26.52 6.60 13.288 71.286 0.154 5.709 19.88 26.54 6.66 13.383 71.360 0.176 5.708 19.85 26.56 6.71 13.469 71.422 0.198 5.707 19.82 26.56 6.74 13.547 71.476 0.220 5.707 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.022 Accepted refinement result: 20.96 26.62 5.67 11.215 71.171 0.022 5.743 Individual atomic B min max mean iso aniso Overall: 29.30 113.86 63.73 5.42 3690 0 Protein: 29.30 113.86 63.73 5.42 3690 0 Chain A: 33.17 113.86 71.50 N/A 1602 0 Chain B: 29.30 111.72 57.77 N/A 2088 0 Histogram: Values Number of atoms 29.30 - 37.76 58 37.76 - 46.21 338 46.21 - 54.67 713 54.67 - 63.12 920 63.12 - 71.58 649 71.58 - 80.03 403 80.03 - 88.49 305 88.49 - 96.95 214 96.95 - 105.40 78 105.40 - 113.86 12 =========================== Idealize ADP of riding H ========================== r_work=0.2096 r_free=0.2662 r_work=0.2097 r_free=0.2664 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2097 r_free= 0.2664 coordinate error (max.-lik. estimate): 0.53 A | | | | normalized target function (ml) (work): 5.742958 | | target function (ml) not normalized (work): 56947.171933 | | target function (ml) not normalized (free): 3153.128589 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2126 0.2097 0.2664 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4105 0.4087 0.4459 n_refl.: 10449 remove outliers: r(all,work,free)=0.4105 0.4087 0.4459 n_refl.: 10449 overall B=0.00 to atoms: r(all,work,free)=0.4105 0.4087 0.4459 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2124 0.2096 0.2653 n_refl.: 10449 remove outliers: r(all,work,free)=0.2124 0.2096 0.2653 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2043 873.044 852.508 1.347 1.110 0.400 14.512-11.594 100.00 95 5 0.1324 830.902 824.266 1.157 1.103 0.378 11.568-9.227 100.00 193 11 0.1301 802.879 791.079 1.138 1.093 0.373 9.162-7.352 100.00 368 15 0.1698 531.905 523.179 1.093 1.075 0.370 7.349-5.862 100.00 740 33 0.2016 393.277 386.993 0.976 1.050 0.350 5.858-4.671 100.00 1425 79 0.1842 421.345 409.703 0.964 1.009 0.290 4.669-3.723 99.86 2790 156 0.2033 387.089 376.715 1.150 0.944 0.200 3.723-3.092 99.93 4210 230 0.2669 211.362 199.782 1.256 0.856 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=0.6617 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2096 r_free=0.2653 After: r_work=0.2096 r_free=0.2653 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.505636 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.044175 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.2096 0.2653 0.0557 0.002 0.6 5.2 0.4 1.9 0 0.125 0.2093 0.2652 0.0560 0.003 0.6 5.1 0.4 1.9 0 0.250 0.2059 0.2650 0.0592 0.007 0.7 5.5 0.4 1.9 0 0.500 0.1987 0.2689 0.0702 0.013 1.3 8.3 0.4 2.6 0 1.000 0.1942 0.2708 0.0766 0.016 1.7 17.5 0.4 5.0 0 2.000 0.1903 0.2722 0.0818 0.020 2.2 19.3 0.6 5.3 0 3.000 0.1885 0.2732 0.0847 0.024 2.6 22.0 0.9 5.8 0 4.000 0.1863 0.2740 0.0877 0.028 2.9 23.7 0.9 7.4 0 5.000 0.1847 0.2744 0.0897 0.031 3.2 27.5 1.3 8.6 0 6.000 0.1837 0.2747 0.0910 0.034 3.5 30.5 1.3 9.8 0 7.000 0.1831 0.2756 0.0925 0.035 3.6 28.9 1.3 8.6 1 8.000 0.1822 0.2777 0.0955 0.039 3.8 33.1 1.3 10.8 1 9.000 0.1810 0.2787 0.0977 0.041 4.1 34.0 1.9 11.5 1 10.000 0.1939 0.2714 0.0775 0.016 1.8 13.5 0.4 3.6 0 1.753 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2093 0.2652 0.0560 0.003 0.6 5.1 0.4 1.9 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.93 26.52 5.60 10.046 70.279 0.044 5.865 24.06 28.36 4.30 8.601 74.093 0.001 5.940 22.08 26.61 4.53 10.288 70.120 0.006 5.891 20.93 26.52 5.60 10.046 70.279 0.022 5.865 20.93 26.52 5.60 10.046 70.279 0.044 5.865 20.64 26.46 5.82 10.679 69.936 0.066 5.854 19.94 26.22 6.28 12.682 70.186 0.088 5.828 19.80 26.28 6.48 13.115 70.480 0.110 5.825 19.82 26.30 6.48 12.881 70.352 0.133 5.826 19.76 26.34 6.58 13.121 70.500 0.155 5.824 19.72 26.36 6.64 13.246 70.571 0.177 5.824 19.67 26.39 6.72 13.515 70.710 0.199 5.822 19.63 26.42 6.79 13.713 70.807 0.221 5.822 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.066 Accepted refinement result: 20.64 26.46 5.82 10.679 69.936 0.066 5.854 Individual atomic B min max mean iso aniso Overall: 25.25 114.63 63.04 6.44 3690 0 Protein: 25.25 114.63 63.04 6.44 3690 0 Chain A: 30.67 114.49 70.80 N/A 1602 0 Chain B: 25.25 114.63 57.08 N/A 2088 0 Histogram: Values Number of atoms 25.25 - 34.19 47 34.19 - 43.12 263 43.12 - 52.06 646 52.06 - 61.00 915 61.00 - 69.94 724 69.94 - 78.88 445 78.88 - 87.81 321 87.81 - 96.75 233 96.75 - 105.69 82 105.69 - 114.63 14 =========================== Idealize ADP of riding H ========================== r_work=0.2064 r_free=0.2646 r_work=0.2062 r_free=0.2647 ----------X-ray data---------- |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2062 r_free= 0.2647 coordinate error (max.-lik. estimate): 0.53 A | | | | normalized target function (ml) (work): 5.853168 | | target function (ml) not normalized (work): 58040.018565 | | target function (ml) not normalized (free): 3216.569909 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 30.50 - 4.90 1.00 2530 123 0.1769 0.2185 6.1253 6.1737| | 2: 4.90 - 3.90 1.00 2451 133 0.1895 0.2494 6.004 6.3462| | 3: 3.89 - 3.40 1.00 2475 150 0.2321 0.2857 5.8121 5.992| | 4: 3.40 - 3.09 1.00 2460 127 0.2884 0.3850 5.4643 5.6249| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 30.50 - 4.90 2530 123 0.86 21.34 1.00 0.92 33398.43| | 2: 4.90 - 3.90 2451 133 0.84 22.85 1.01 0.96 30282.96| | 3: 3.89 - 3.40 2475 150 0.75 31.67 1.02 0.90 24189.95| | 4: 3.40 - 3.09 2460 127 0.65 40.37 0.90 0.75 15119.40| |alpha: min = 0.75 max = 0.96 mean = 0.88| |beta: min = 15119.40 max = 33398.43 mean = 25795.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.78| |phase err.(work): min = 0.00 max = 89.96 mean = 29.01| |phase err.(test): min = 0.00 max = 86.26 mean = 29.87| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2092 0.2062 0.2647 n_refl.: 10449 re-set all scales: r(all,work,free)=0.4045 0.4026 0.4412 n_refl.: 10449 remove outliers: r(all,work,free)=0.4045 0.4026 0.4412 n_refl.: 10449 overall B=0.00 to atoms: r(all,work,free)=0.4045 0.4026 0.4412 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2086 0.2056 0.2651 n_refl.: 10449 remove outliers: r(all,work,free)=0.2086 0.2056 0.2651 n_refl.: 10449 ======================== 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 30.500-14.559 100.00 95 4 0.2046 873.044 854.193 1.382 1.133 0.406 14.512-11.594 100.00 95 5 0.1314 830.902 822.857 1.165 1.123 0.379 11.568-9.227 100.00 193 11 0.1299 802.879 790.076 1.145 1.111 0.373 9.162-7.352 100.00 368 15 0.1685 531.905 522.586 1.100 1.090 0.370 7.349-5.862 100.00 740 33 0.2000 393.277 386.620 0.985 1.061 0.350 5.858-4.671 100.00 1425 79 0.1819 421.345 409.624 0.985 1.012 0.300 4.669-3.723 99.86 2790 156 0.1979 387.089 377.076 1.180 0.935 0.210 3.723-3.092 99.93 4210 230 0.2608 211.362 199.743 1.297 0.831 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=2.1524 ================= 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 : 0.3804 0.4305 0.010 1.710 15.7 95.5 52.2 0 0.000 1_bss: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_settarget: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_updatephipsi: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_weight: 0.2260 0.2819 0.010 1.710 32.0 111.9 68.6 0 0.000 1_xyzrec: 0.2309 0.2727 0.003 0.639 32.0 111.9 68.6 0 0.195 1_adp: 0.2107 0.2685 0.003 0.639 36.1 120.3 70.3 0 0.195 1_regHadp: 0.2084 0.2670 0.003 0.639 36.1 120.3 70.3 0 0.195 2_bss: 0.2096 0.2711 0.003 0.639 30.1 114.3 64.2 0 0.195 2_settarget: 0.2096 0.2711 0.003 0.639 30.1 114.3 64.2 0 0.195 2_updatephipsi: 0.2096 0.2711 0.003 0.639 30.1 114.3 64.2 0 0.195 2_updatecdl: 0.2096 0.2711 0.003 0.683 30.1 114.3 64.2 0 0.195 2_weight: 0.2096 0.2711 0.003 0.683 30.1 114.3 64.2 0 0.195 2_xyzrec: 0.2086 0.2670 0.002 0.555 30.1 114.3 64.2 0 0.231 2_adp: 0.2096 0.2662 0.002 0.555 29.3 113.9 63.7 0 0.231 2_regHadp: 0.2097 0.2664 0.002 0.555 29.3 113.9 63.7 0 0.231 3_bss: 0.2096 0.2653 0.002 0.555 29.3 113.9 63.7 0 0.231 3_settarget: 0.2096 0.2653 0.002 0.555 29.3 113.9 63.7 0 0.231 3_updatephipsi: 0.2096 0.2653 0.002 0.555 29.3 113.9 63.7 0 0.231 3_updatecdl: 0.2096 0.2653 0.003 0.575 29.3 113.9 63.7 0 0.231 3_setrh: 0.2096 0.2653 0.003 0.575 29.3 113.9 63.7 0 0.231 3_weight: 0.2096 0.2653 0.003 0.575 29.3 113.9 63.7 0 0.231 3_xyzrec: 0.2093 0.2652 0.003 0.559 29.3 113.9 63.7 0 0.231 3_adp: 0.2064 0.2646 0.003 0.559 25.2 114.6 63.0 0 0.231 3_regHadp: 0.2062 0.2647 0.003 0.559 25.2 114.6 63.0 0 0.231 end: 0.2056 0.2651 0.003 0.559 25.2 114.6 63.0 0 0.231 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1m10_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1m10_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 11.0700 Refinement macro-cycles (run) : 291.9500 Write final files (write_after_run_outputs) : 21.4600 Total : 324.4800 Total CPU time: 6.13 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:12 PDT -0700 (1716251712.71 s) Start R-work = 0.2260, R-free = 0.2819 Final R-work = 0.2056, R-free = 0.2651 =============================================================================== Job complete usr+sys time: 385.20 seconds wall clock time: 18 minutes 27.10 seconds (1107.10 seconds total)