Starting phenix.refine on Mon May 20 17:15:26 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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } 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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } 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: 0.58, per 1000 atoms: 0.19 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: 0.67 Conformation dependent library (CDL) restraints added in 99.8 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 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id= A, first strand: chain 'A' and resid 64 through 71 removed outlier: 5.403A pdb=" N VAL A 5 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE A 108 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 44 removed outlier: 3.804A pdb=" N GLY A 41 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A 43 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= D, first strand: chain 'B' and resid 3 through 9 removed outlier: 3.564A pdb=" N GLY B 33 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 42 through 44 Processing sheet with id= F, first strand: chain 'B' and resid 45 through 47 59 hydrogen bonds defined for protein. 162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.60 Time building geometry restraints manager: 0.78 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: 144 2.08 - 2.69: 4346 2.69 - 3.29: 8486 3.29 - 3.90: 10882 3.90 - 4.50: 16220 Nonbonded interactions: 40078 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=" 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 nonbonded pdb=" O ASP A 60 " pdb=" H GLY A 63 " model vdw 1.652 1.850 ... (remaining 40073 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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { sheet { first_strand = chain 'A' and resid 64 through 71 sheet_id = " A" strand { selection = chain 'A' and resid 29 through 36 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 35 and name N bond_start_previous = chain 'A' and resid 65 and name O } strand { selection = chain 'A' and resid 15 through 21 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 19 and name N bond_start_previous = chain 'A' and resid 32 and name O } strand { selection = chain 'A' and resid 3 through 9 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 8 and name N bond_start_previous = chain 'A' and resid 16 and name O } strand { selection = chain 'A' and resid 107 through 110 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 110 and name N bond_start_previous = chain 'A' and resid 3 and name O } } sheet { first_strand = chain 'A' and resid 41 through 44 sheet_id = " B" strand { selection = chain 'A' and resid 56 through 59 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 59 and name N bond_start_previous = chain 'A' and resid 41 and name O } } sheet { first_strand = chain 'A' and resid 45 through 47 sheet_id = " C" strand { selection = chain 'A' and resid 86 through 90 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 88 and name N bond_start_previous = chain 'A' and resid 46 and name O } strand { selection = chain 'A' and resid 101 through 105 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 104 and name N bond_start_previous = chain 'A' and resid 87 and name O } } sheet { first_strand = chain 'B' and resid 3 through 9 sheet_id = " D" strand { selection = chain 'B' and resid 15 through 22 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 20 and name N bond_start_previous = chain 'B' and resid 4 and name O } strand { selection = chain 'B' and resid 29 through 36 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 36 and name N bond_start_previous = chain 'B' and resid 15 and name O } strand { selection = chain 'B' and resid 66 through 71 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 71 and name N bond_start_previous = chain 'B' and resid 29 and name O } } sheet { first_strand = chain 'B' and resid 42 through 44 sheet_id = " E" strand { selection = chain 'B' and resid 56 through 58 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 57 and name N bond_start_previous = chain 'B' and resid 43 and name O } } sheet { first_strand = chain 'B' and resid 45 through 47 sheet_id = " F" strand { selection = chain 'B' and resid 86 through 90 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 88 and name N bond_start_previous = chain 'B' and resid 46 and name O } strand { selection = chain 'B' and resid 101 through 105 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 104 and name N bond_start_previous = chain 'B' and resid 87 and name O } } } enabled = True } 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= 0.351 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. ================================== NQH flips ================================== r_work=0.2035 r_free=0.2627 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2035 r_free=0.2627 ========================= Local real-space refinement ========================= Before: r_work=0.2035 r_free=0.2627 67 residues out of total 156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.114 outliers start: 6 outliers final: 3 residues processed: 6 average time/residue: 0.1354 time to fit residues: 1.0908 After: r_work=0.2048 r_free=0.2629 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.990036 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.265547 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 0.2232 0.2743 0.0511 0.002 0.5 1.6 0.0 2.6 0 0.125 0.2150 0.2712 0.0562 0.002 0.5 1.6 0.0 3.2 0 0.250 0.2104 0.2736 0.0632 0.003 0.6 1.9 0.0 3.2 0 0.500 0.2031 0.2807 0.0776 0.004 0.6 2.9 0.0 3.2 0 1.000 0.1925 0.2878 0.0954 0.005 0.8 5.2 0.0 6.4 0 2.000 0.1866 0.2938 0.1072 0.007 0.9 6.8 0.0 7.7 0 3.000 0.1825 0.2968 0.1144 0.008 1.0 8.8 0.0 7.7 0 4.000 0.1789 0.2981 0.1192 0.010 1.1 11.0 0.0 8.3 0 5.000 0.1764 0.2986 0.1222 0.011 1.2 11.3 0.0 8.3 0 6.000 0.1743 0.2988 0.1245 0.013 1.3 13.0 0.0 10.3 0 7.000 0.1732 0.2979 0.1248 0.014 1.3 13.9 0.0 10.9 0 8.000 0.1711 0.2986 0.1275 0.015 1.4 13.9 0.0 10.9 0 9.000 0.1697 0.2968 0.1271 0.016 1.5 14.6 0.0 11.5 0 10.000 0.1757 0.2983 0.1226 0.012 1.2 13.0 0.0 10.3 0 6.495 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2150 0.2712 0.0562 0.002 0.5 1.6 0.0 3.2 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2150 r_free=0.2712 63 residues out of total 156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.114 outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0356 time to fit residues: 0.4106 After: r_work=0.2201 r_free=0.2783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.01 27.83 5.83 8.919 45.386 0.266 0.064 22.14 28.26 6.11 8.142 45.914 0.008 0.064 21.16 27.97 6.80 8.630 45.673 0.033 0.059 20.55 27.73 7.17 9.255 45.517 0.133 0.056 19.77 27.55 7.78 10.121 45.835 0.266 0.052 18.45 27.37 8.92 12.657 46.759 0.398 0.046 18.18 27.39 9.21 13.424 47.042 0.531 0.045 17.98 27.39 9.41 14.049 47.276 0.664 0.044 17.66 27.39 9.73 15.008 47.698 0.797 0.043 17.14 27.43 10.29 16.744 48.475 0.929 0.040 17.01 27.44 10.43 17.288 48.678 1.062 0.040 16.87 27.45 10.58 17.865 48.903 1.195 0.039 16.77 27.47 10.70 18.286 49.058 1.328 0.039 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: 22.14 28.26 6.11 8.142 45.914 0.008 0.064 Individual atomic B min max mean iso aniso Overall: 35.44 78.74 49.93 1.34 1542 0 Protein: 35.44 78.74 49.93 1.34 1542 0 Chain A: 35.44 74.47 47.68 N/A 771 0 Chain B: 36.55 78.74 52.17 N/A 771 0 Histogram: Values Number of atoms 35.44 - 39.77 192 39.77 - 44.10 262 44.10 - 48.43 238 48.43 - 52.76 260 52.76 - 57.09 313 57.09 - 61.42 140 61.42 - 65.75 86 65.75 - 70.08 21 70.08 - 74.41 20 74.41 - 78.74 10 =========================== Idealize ADP of riding H ========================== r_work=0.2214 r_free=0.2826 r_work=0.2208 r_free=0.2780 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.2208 r_free= 0.2780 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ls_wunit_k1) (work): 0.063719 | | target function (ls_wunit_k1) not normalized (work): 125.717203 | | target function (ls_wunit_k1) not normalized (free): 22.184539 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2264 0.2208 0.2780 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4529 0.4534 0.4523 n_refl.: 2192 remove outliers: r(all,work,free)=0.4529 0.4534 0.4523 n_refl.: 2192 overall B=1.61 to atoms: r(all,work,free)=0.4590 0.4596 0.4566 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2222 0.2169 0.2704 n_refl.: 2192 remove outliers: r(all,work,free)=0.2222 0.2169 0.2704 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 0.2080 488.759 472.416 1.122 1.192 0.376 10.083-8.012 89.47 92 10 0.2232 325.444 314.603 1.031 1.146 0.381 8.010-6.369 93.43 180 19 0.2470 308.840 295.652 0.998 1.104 0.379 6.360-5.059 92.00 354 37 0.2066 302.460 286.763 0.916 1.042 0.375 5.057-4.020 93.48 707 82 0.2075 315.858 300.332 1.052 0.943 0.279 4.017-3.602 94.20 556 61 0.2295 229.446 208.736 1.170 0.848 0.272 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=7.2311 ============================ 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 ============================ ================================== NQH flips ================================== r_work=0.2169 r_free=0.2704 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS Total number of N/Q/H flips: 1 r_work=0.2168 r_free=0.2699 ========================= Local real-space refinement ========================= Before: r_work=0.2168 r_free=0.2699 60 residues out of total 156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.118 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1389 After: r_work=0.2168 r_free=0.2699 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.156428 wxc_scale = 0.026 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.043810 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 0.2360 0.2845 0.0485 0.002 0.4 3.2 0.0 1.3 0 0.006 0.2296 0.2812 0.0516 0.002 0.4 2.9 0.0 1.3 0 0.017 0.2207 0.2757 0.0550 0.002 0.4 2.9 0.0 1.3 0 0.033 0.2154 0.2707 0.0553 0.002 0.5 2.6 0.0 1.3 0 0.050 0.2115 0.2702 0.0588 0.002 0.5 2.9 0.0 1.3 0 0.067 0.2084 0.2695 0.0611 0.002 0.5 2.9 0.0 1.9 0 0.083 0.2051 0.2691 0.0640 0.002 0.5 2.6 0.0 1.9 0 0.100 0.2026 0.2703 0.0678 0.002 0.5 3.6 0.0 1.9 0 0.117 0.2139 0.2713 0.0574 0.002 0.5 3.2 0.0 1.3 0 0.056 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2051 0.2691 0.0640 0.002 0.5 2.6 0.0 1.9 0 0.100 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2051 r_free=0.2691 67 residues out of total 156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.205 outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0549 time to fit residues: 0.4281 After: r_work=0.2082 r_free=0.2732 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.82 27.32 6.50 7.155 56.310 0.044 5.658 21.13 27.96 6.83 7.158 57.224 0.001 5.672 19.58 27.29 7.70 7.440 56.625 0.005 5.597 17.83 27.12 9.29 8.873 57.420 0.022 5.503 17.52 27.10 9.58 9.575 57.513 0.044 5.485 17.32 27.12 9.80 10.098 57.702 0.066 5.473 17.12 27.12 10.00 10.677 57.942 0.088 5.461 16.98 27.13 10.15 11.134 58.123 0.110 5.453 16.68 27.10 10.43 12.256 58.555 0.131 5.434 16.59 27.10 10.51 12.688 58.706 0.153 5.429 16.54 27.11 10.57 12.977 58.807 0.175 5.426 16.45 27.12 10.66 13.435 58.958 0.197 5.421 16.44 27.13 10.69 13.532 58.996 0.219 5.420 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.001 Accepted refinement result: 21.13 27.96 6.83 7.158 57.224 0.001 5.672 Individual atomic B min max mean iso aniso Overall: 42.59 75.35 53.36 1.29 1542 0 Protein: 42.59 75.35 53.36 1.29 1542 0 Chain A: 42.59 71.08 51.55 N/A 771 0 Chain B: 44.31 75.35 55.17 N/A 771 0 Histogram: Values Number of atoms 42.59 - 45.87 69 45.87 - 49.14 232 49.14 - 52.42 423 52.42 - 55.70 386 55.70 - 58.97 236 58.97 - 62.25 123 62.25 - 65.52 38 65.52 - 68.80 13 68.80 - 72.08 18 72.08 - 75.35 4 =========================== Idealize ADP of riding H ========================== r_work=0.2113 r_free=0.2796 r_work=0.2118 r_free=0.2795 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.2118 r_free= 0.2795 coordinate error (max.-lik. estimate): 0.42 A | | | | normalized target function (ml) (work): 5.674176 | | target function (ml) not normalized (work): 11195.149250 | | target function (ml) not normalized (free): 1324.076073 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2185 0.2118 0.2795 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4686 0.4688 0.4684 n_refl.: 2192 remove outliers: r(all,work,free)=0.4686 0.4688 0.4684 n_refl.: 2192 overall B=0.00 to atoms: r(all,work,free)=0.4686 0.4688 0.4684 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2204 0.2133 0.2854 n_refl.: 2192 remove outliers: r(all,work,free)=0.2204 0.2133 0.2854 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 0.2143 488.759 471.158 1.268 1.051 0.376 10.083-8.012 89.47 92 10 0.2364 325.444 313.886 1.129 1.033 0.380 8.010-6.369 93.43 180 19 0.2553 308.840 294.845 1.074 1.020 0.380 6.360-5.059 92.00 354 37 0.2104 302.460 285.088 0.935 1.004 0.350 5.057-4.020 93.48 707 82 0.2008 315.858 300.970 1.035 0.978 0.250 4.017-3.602 94.20 556 61 0.2124 229.446 210.450 1.067 0.956 0.250 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.1477 ============================ 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=0.2133 r_free=0.2854 After: r_work=0.2133 r_free=0.2854 ================================== NQH flips ================================== r_work=0.2133 r_free=0.2854 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS Total number of N/Q/H flips: 1 r_work=0.2131 r_free=0.2853 ========================= Local real-space refinement ========================= Before: r_work=0.2131 r_free=0.2853 62 residues out of total 156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.493 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5490 After: r_work=0.2131 r_free=0.2853 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.132391 wxc_scale = 0.054 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.037895 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 0.2136 0.2813 0.0677 0.003 0.5 3.2 0.0 0.0 0 0.012 0.2131 0.2811 0.0680 0.003 0.5 3.2 0.0 0.0 0 0.035 0.2125 0.2809 0.0684 0.003 0.5 3.2 0.0 0.0 0 0.069 0.2120 0.2807 0.0686 0.003 0.5 3.2 0.0 0.0 0 0.104 0.2113 0.2807 0.0694 0.003 0.5 3.6 0.0 0.0 0 0.138 0.2100 0.2807 0.0708 0.004 0.6 3.2 0.0 0.0 0 0.173 0.2076 0.2812 0.0736 0.006 0.6 3.6 0.0 0.0 0 0.208 0.2049 0.2813 0.0765 0.007 0.7 3.6 0.0 0.0 0 0.242 0.2117 0.2807 0.0690 0.003 0.5 3.2 0.0 0.0 0 0.115 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2120 0.2807 0.0686 0.003 0.5 3.2 0.0 0.0 0 0.104 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2120 r_free=0.2807 59 residues out of total 156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.493 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3838 After: r_work=0.2120 r_free=0.2807 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.20 28.07 6.86 7.605 58.654 0.038 5.675 21.40 28.18 6.78 5.471 60.825 0.001 5.683 20.23 27.94 7.72 7.838 58.741 0.005 5.629 18.19 27.28 9.09 8.978 59.895 0.019 5.522 17.87 27.40 9.53 9.646 59.925 0.038 5.503 17.49 27.32 9.83 10.509 60.299 0.057 5.480 17.43 27.39 9.96 10.764 60.350 0.076 5.476 17.07 27.26 10.19 11.834 60.808 0.095 5.455 17.16 27.36 10.21 11.618 60.690 0.114 5.460 17.06 27.35 10.29 11.931 60.809 0.133 5.454 16.79 27.24 10.46 13.072 61.247 0.152 5.437 16.72 27.24 10.52 13.419 61.364 0.171 5.433 16.68 27.24 10.56 13.677 61.452 0.189 5.430 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.001 Accepted refinement result: 21.40 28.18 6.78 5.471 60.825 0.001 5.683 Individual atomic B min max mean iso aniso Overall: 49.45 70.35 57.71 0.88 1542 0 Protein: 49.45 70.35 57.71 0.88 1542 0 Chain A: 49.45 67.37 56.84 N/A 771 0 Chain B: 50.67 70.35 58.57 N/A 771 0 Histogram: Values Number of atoms 49.45 - 51.54 43 51.54 - 53.63 254 53.63 - 55.72 274 55.72 - 57.81 258 57.81 - 59.90 260 59.90 - 61.99 182 61.99 - 64.08 142 64.08 - 66.17 99 66.17 - 68.26 25 68.26 - 70.35 5 =========================== Idealize ADP of riding H ========================== r_work=0.2140 r_free=0.2818 r_work=0.2142 r_free=0.2814 ----------X-ray data---------- |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.2142 r_free= 0.2814 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 5.683683 | | target function (ml) not normalized (work): 11213.906756 | | target function (ml) not normalized (free): 1326.729105 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2150 0.2765 5.7949 6.0566| | 2: 4.53 - 3.60 0.94 993 110 0.2133 0.2871 5.5739 6.0596| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.87 20.23 0.99 1.05 17244.83| | 2: 4.53 - 3.60 993 110 0.90 17.69 1.02 1.07 9675.51| |alpha: min = 1.01 max = 1.12 mean = 1.06| |beta: min = 7533.90 max = 24831.97 mean = 13435.23| |figures of merit: min = 0.00 max = 1.00 mean = 0.88| |phase err.(work): min = 0.00 max = 90.00 mean = 18.95| |phase err.(test): min = 0.00 max = 77.05 mean = 18.71| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2209 0.2142 0.2814 n_refl.: 2192 re-set all scales: r(all,work,free)=0.4867 0.4872 0.4827 n_refl.: 2192 remove outliers: r(all,work,free)=0.4867 0.4872 0.4827 n_refl.: 2192 overall B=-2.09 to atoms: r(all,work,free)=0.4787 0.4791 0.4770 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2189 0.2119 0.2824 n_refl.: 2192 remove outliers: r(all,work,free)=0.2189 0.2119 0.2824 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 0.2118 488.759 468.733 1.063 1.162 0.371 10.083-8.012 89.47 92 10 0.2371 325.444 313.428 0.965 1.121 0.370 8.010-6.369 93.43 180 19 0.2543 308.840 292.553 0.942 1.086 0.364 6.360-5.059 92.00 354 37 0.2085 302.460 285.120 0.872 1.033 0.346 5.057-4.020 93.48 707 82 0.1978 315.858 302.090 1.035 0.949 0.241 4.017-3.602 94.20 556 61 0.2149 229.446 210.898 1.152 0.869 0.239 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.4583 ================= 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_nqh: 0.2035 0.2627 0.005 1.074 29.5 83.7 48.9 0 0.000 1_realsrl: 0.2048 0.2629 0.005 1.074 29.5 83.7 48.9 0 0.014 1_weight: 0.2048 0.2629 0.005 1.074 29.5 83.7 48.9 0 0.014 1_xyzrec: 0.2150 0.2712 0.002 0.522 29.5 83.7 48.9 0 0.166 1_realsrl2: 0.2201 0.2783 0.002 0.522 29.5 83.7 48.9 0 0.174 1_adp: 0.2214 0.2826 0.002 0.522 35.4 78.7 49.9 0 0.174 1_regHadp: 0.2208 0.2780 0.002 0.522 35.4 78.7 49.9 0 0.174 2_bss: 0.2169 0.2704 0.002 0.522 37.0 80.4 51.5 0 0.174 2_settarget: 0.2169 0.2704 0.002 0.522 37.0 80.4 51.5 0 0.174 2_updatephipsi: 0.2169 0.2704 0.002 0.522 37.0 80.4 51.5 0 0.174 2_updatecdl: 0.2169 0.2704 0.002 0.551 37.0 80.4 51.5 0 0.174 2_nqh: 0.2168 0.2699 0.002 0.551 37.0 80.4 51.5 0 0.178 2_realsrl: 0.2168 0.2699 0.002 0.551 37.0 80.4 51.5 0 0.178 2_weight: 0.2168 0.2699 0.002 0.551 37.0 80.4 51.5 0 0.178 2_xyzrec: 0.2051 0.2691 0.002 0.504 37.0 80.4 51.5 0 0.224 2_realsrl2: 0.2082 0.2732 0.002 0.504 37.0 80.4 51.5 0 0.226 2_adp: 0.2113 0.2796 0.002 0.504 42.6 75.4 53.4 0 0.226 2_regHadp: 0.2118 0.2795 0.002 0.504 42.6 75.4 53.4 0 0.226 3_bss: 0.2133 0.2854 0.002 0.504 42.6 75.4 53.4 0 0.226 3_settarget: 0.2133 0.2854 0.002 0.504 42.6 75.4 53.4 0 0.226 3_updatephipsi: 0.2133 0.2854 0.002 0.504 42.6 75.4 53.4 0 0.226 3_updatecdl: 0.2133 0.2854 0.002 0.522 42.6 75.4 53.4 0 0.226 3_setrh: 0.2133 0.2854 0.002 0.522 42.6 75.4 53.4 0 0.226 3_nqh: 0.2131 0.2853 0.002 0.522 42.6 75.4 53.4 0 0.231 3_realsrl: 0.2131 0.2853 0.002 0.522 42.6 75.4 53.4 0 0.231 3_weight: 0.2131 0.2853 0.002 0.522 42.6 75.4 53.4 0 0.231 3_xyzrec: 0.2120 0.2807 0.003 0.521 42.6 75.4 53.4 0 0.232 3_realsrl2: 0.2120 0.2807 0.003 0.521 42.6 75.4 53.4 0 0.232 3_adp: 0.2140 0.2818 0.003 0.521 49.4 70.4 57.7 0 0.232 3_regHadp: 0.2142 0.2814 0.003 0.521 49.4 70.4 57.7 0 0.232 end: 0.2119 0.2824 0.003 0.521 47.4 68.3 55.6 0 0.232 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/4xcr_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/4xcr_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.3400 Refinement macro-cycles (run) : 110.5300 Write final files (write_after_run_outputs) : 13.2700 Total : 126.1400 Total CPU time: 2.36 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:19:58 PDT -0700 (1716250798.27 s) Start R-work = 0.2035, R-free = 0.2627 Final R-work = 0.2119, R-free = 0.2824 =============================================================================== Job complete usr+sys time: 149.58 seconds wall clock time: 4 minutes 54.86 seconds (294.86 seconds total)