Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fb5.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.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=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fb5.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fb5.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 { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 5100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5082 Classifications: {'peptide': 320} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Classifications: {'peptide': 1} Modifications used: {'NH3': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.36 Number of scatterers: 5100 At special positions: 0 Unit cell: (184.7, 184.7, 184.7, 90, 90, 90) Space group: P 43 3 2 (No. 212) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 476 8.00 N 427 7.00 C 1617 6.00 H 2569 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: 4.74 Conformation dependent library (CDL) restraints added in 564.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 602 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 2 sheets defined 44.2% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 50 through 68 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 91 through 103 Processing helix chain 'A' and resid 124 through 133 removed outlier: 4.739A pdb=" N ARG A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 199 through 211 removed outlier: 4.450A pdb=" N ALA A 209 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LYS A 210 " --> pdb=" O MET A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.937A pdb=" N LEU A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.026A pdb=" N VAL A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 323 through 342 removed outlier: 4.539A pdb=" N LYS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 107 through 111 Processing sheet with id= B, first strand: chain 'A' and resid 299 through 301 removed outlier: 3.539A pdb=" N VAL A 259 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 263 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N HIS A 214 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TRP A 193 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN A 216 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N GLY A 195 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ALA A 218 " --> pdb=" O GLY A 195 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 245 " --> pdb=" O LEU A 215 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 282 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: 3.26 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 565 1.05 - 1.25: 2357 1.25 - 1.44: 743 1.44 - 1.64: 1466 1.64 - 1.83: 20 Bond restraints: 5151 Sorted by residual: bond pdb=" NH2 ARG A 94 " pdb="HH22 ARG A 94 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" ND1 HIS A 117 " pdb=" HD1 HIS A 117 " 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 253 " pdb=" H ALA A 253 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS A 168 " pdb=" HE2 HIS A 168 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LYS A 275 " pdb=" H LYS A 275 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 5146 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.38: 128 105.38 - 112.52: 5958 112.52 - 119.66: 1333 119.66 - 126.80: 1893 126.80 - 133.95: 34 Bond angle restraints: 9346 Sorted by residual: angle pdb=" N ALA A 280 " pdb=" CA ALA A 280 " pdb=" C ALA A 280 " ideal model delta sigma weight residual 113.38 99.63 13.75 1.23e+00 6.61e-01 1.25e+02 angle pdb=" N GLN A 279 " pdb=" CA GLN A 279 " pdb=" C GLN A 279 " ideal model delta sigma weight residual 114.09 99.75 14.34 1.55e+00 4.16e-01 8.56e+01 angle pdb=" N GLN A 145 " pdb=" CA GLN A 145 " pdb=" C GLN A 145 " ideal model delta sigma weight residual 110.97 101.49 9.48 1.09e+00 8.42e-01 7.57e+01 angle pdb=" N LEU A 186 " pdb=" CA LEU A 186 " pdb=" C LEU A 186 " ideal model delta sigma weight residual 113.72 103.13 10.59 1.30e+00 5.92e-01 6.64e+01 angle pdb=" N ALA A 253 " pdb=" CA ALA A 253 " pdb=" C ALA A 253 " ideal model delta sigma weight residual 113.41 104.47 8.94 1.22e+00 6.72e-01 5.37e+01 ... (remaining 9341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 2174 22.04 - 44.07: 165 44.07 - 66.11: 60 66.11 - 88.14: 7 88.14 - 110.18: 2 Dihedral angle restraints: 2408 sinusoidal: 1323 harmonic: 1085 Sorted by residual: dihedral pdb=" CG NVA A 900 " pdb=" CA NVA A 900 " pdb=" CB NVA A 900 " pdb=" HA NVA A 900 " ideal model delta sinusoidal sigma weight residual -62.82 47.36 -110.18 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" N GLN A 348 " pdb=" C GLN A 348 " pdb=" CA GLN A 348 " pdb=" CB GLN A 348 " ideal model delta harmonic sigma weight residual 122.80 114.22 8.58 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" CG ARG A 40 " pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " ideal model delta sinusoidal sigma weight residual -90.00 -43.56 -46.44 2 1.50e+01 4.44e-03 1.12e+01 ... (remaining 2405 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.077: 254 0.077 - 0.153: 94 0.153 - 0.229: 35 0.229 - 0.306: 10 0.306 - 0.382: 4 Chirality restraints: 397 Sorted by residual: chirality pdb=" CA TRP A 298 " pdb=" N TRP A 298 " pdb=" C TRP A 298 " pdb=" CB TRP A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASN A 329 " pdb=" N ASN A 329 " pdb=" C ASN A 329 " pdb=" CB ASN A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ALA A 280 " pdb=" N ALA A 280 " pdb=" C ALA A 280 " pdb=" CB ALA A 280 " both_signs ideal model delta sigma weight residual False 2.48 2.80 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 394 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 298 " -0.117 2.00e-02 2.50e+03 3.53e-02 5.00e+01 pdb=" CG TRP A 298 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 298 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 298 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 298 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 298 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 298 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 298 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 298 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 298 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP A 298 " 0.039 2.00e-02 2.50e+03 pdb=" HE1 TRP A 298 " -0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP A 298 " 0.036 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 298 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 298 " 0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP A 298 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 193 " -0.080 2.00e-02 2.50e+03 2.41e-02 2.33e+01 pdb=" CG TRP A 193 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 193 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 193 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 193 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 193 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 193 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 193 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 193 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TRP A 193 " -0.007 2.00e-02 2.50e+03 pdb=" HE3 TRP A 193 " 0.025 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 193 " -0.016 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 193 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 193 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 317 " 0.057 2.00e-02 2.50e+03 2.24e-02 1.51e+01 pdb=" CG TYR A 317 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 317 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 317 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 317 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 317 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 317 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 317 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 317 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR A 317 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 317 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 317 " -0.008 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 0.68 - 1.47: 36 1.47 - 2.25: 1116 2.25 - 3.03: 16007 3.03 - 3.82: 23925 3.82 - 4.60: 38499 Warning: very small nonbonded interaction distances. Nonbonded interactions: 79583 Sorted by model distance: nonbonded pdb=" HB3 ARG A 40 " pdb="HH11 ARG A 40 " model vdw 0.684 2.270 nonbonded pdb=" HG2 GLU A 87 " pdb=" HD1 HIS A 117 " model vdw 0.725 2.270 nonbonded pdb="HD13 ILE A 116 " pdb=" HB3 LEU A 124 " model vdw 0.838 2.440 nonbonded pdb=" HA ILE A 116 " pdb="HG21 VAL A 120 " model vdw 0.941 2.440 nonbonded pdb=" OE2 GLU A 122 " pdb=" HB3 PRO A 305 " model vdw sym.op. 0.998 2.620 z,x,y ... (remaining 79578 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 11 15.91 1 O 476 7.97 1 N 427 6.97 1 C 1617 5.97 1 H 2569 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: 2569 of 5100 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 5100 n_use_u_iso = 5100 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 = 5100 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (5100 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 5100 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 { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 45 through 47 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 50 through 68 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 75 through 77 helix_type = alpha pi *3_10 unknown } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 91 through 103 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 124 through 133 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 145 through 153 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 169 through 183 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 199 through 211 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 227 through 240 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 250 through 252 helix_type = alpha pi *3_10 unknown } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 272 through 275 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 277 through 279 helix_type = alpha pi *3_10 unknown } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 288 through 293 } helix { serial_number = "14" helix_identifier = "14" selection = chain 'A' and resid 308 through 310 helix_type = alpha pi *3_10 unknown } helix { serial_number = "15" helix_identifier = "15" selection = chain 'A' and resid 313 through 316 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'A' and resid 323 through 342 } sheet { first_strand = chain 'A' and resid 107 through 111 sheet_id = " A" strand { selection = chain 'A' and resid 81 through 86 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 82 and name N bond_start_previous = chain 'A' and resid 107 and name O } strand { selection = chain 'A' and resid 138 through 141 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 139 and name N bond_start_previous = chain 'A' and resid 83 and name O } strand { selection = chain 'A' and resid 159 through 161 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 160 and name N bond_start_previous = chain 'A' and resid 138 and name O } } sheet { first_strand = chain 'A' and resid 299 through 301 sheet_id = " B" strand { selection = chain 'A' and resid 259 through 263 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 260 and name N bond_start_previous = chain 'A' and resid 299 and name O } strand { selection = chain 'A' and resid 190 through 195 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 192 and name N bond_start_previous = chain 'A' and resid 259 and name O } strand { selection = chain 'A' and resid 214 through 218 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 214 and name N bond_start_previous = chain 'A' and resid 191 and name O } strand { selection = chain 'A' and resid 244 through 247 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 245 and name N bond_start_previous = chain 'A' and resid 215 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1fb5_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2569 occupancy sum: 2569.00 (% of total atoms 50.55) Rotatable: count: 751 occupancy sum: 751.00 (% of total atoms 14.78) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 55.69 A, n_refl.=13583 (all), 5.08 % free)------------| | | | r_work= 0.3934 r_free= 0.3841 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 7.070147 | | target function (ml) not normalized (work): 91155.402602 | | target function (ml) not normalized (free): 4891.182011 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 55.69 - 5.99 0.96 2727 155 0.4383 0.4389 7.8547 7.6803| | 2: 5.98 - 4.75 0.97 2600 136 0.3400 0.3210 7.1228 7.1545| | 3: 4.75 - 4.15 0.98 2607 127 0.3675 0.3564 6.9337 6.9672| | 4: 4.15 - 3.77 0.95 2474 131 0.3917 0.3663 6.7408 6.855| | 5: 3.77 - 3.50 0.96 2485 141 0.4190 0.4058 6.6251 6.7013| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 55.69 - 5.99 2727 155 0.56 45.31 0.74 0.54 772694.27| | 2: 5.98 - 4.75 2600 136 0.62 41.75 1.31 0.69 464297.85| | 3: 4.75 - 4.15 2607 127 0.77 28.66 1.48 0.80 250471.84| | 4: 4.15 - 3.77 2474 131 0.82 24.66 1.52 0.86 130060.96| | 5: 3.77 - 3.50 2485 141 0.79 27.72 1.54 0.87 102817.37| |alpha: min = 0.54 max = 0.87 mean = 0.75| |beta: min = 102817.37 max = 772694.27 mean = 352483.04| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 33.87| |phase err.(test): min = 0.00 max = 89.68 mean = 32.98| |-----------------------------------------------------------------------------| ----------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 0.067 2582 Z= 0.664 Angle : 1.670 14.337 3492 Z= 1.077 Chirality : 0.099 0.382 397 Planarity : 0.008 0.083 441 Dihedral : 17.955 87.743 961 Min Nonbonded Distance : 1.472 Molprobity Statistics. All-atom Clashscore : 64.94 Ramachandran Plot: Outliers : 7.86 % Allowed : 20.75 % Favored : 71.38 % Rotamer: Outliers : 16.73 % Allowed : 15.64 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -6.37 (0.33), residues: 318 helix: -4.89 (0.20), residues: 119 sheet: -2.43 (0.57), residues: 57 loop : -4.35 (0.40), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 94 TYR 0.047 0.010 TYR A 317 PHE 0.031 0.012 PHE A 65 TRP 0.080 0.015 TRP A 298 HIS 0.003 0.001 HIS A 182 Individual atomic B min max mean iso aniso Overall: 9.34 143.19 50.12 1.69 2531 0 Protein: 9.34 143.19 50.12 1.69 2531 0 Chain A: 9.34 143.19 50.12 N/A 2531 0 Histogram: Values Number of atoms 9.34 - 22.73 309 22.73 - 36.11 663 36.11 - 49.50 541 49.50 - 62.88 410 62.88 - 76.27 277 76.27 - 89.65 96 89.65 - 103.03 41 103.03 - 116.42 41 116.42 - 129.81 78 129.81 - 143.19 75 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13583 (all), 5.08 % free)------------| | | | r_work= 0.3934 r_free= 0.3841 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 7.070147 | | target function (ml) not normalized (work): 91155.402602 | | target function (ml) not normalized (free): 4891.182011 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3926 0.3934 0.3841 n_refl.: 13583 re-set all scales: r(all,work,free)=0.3926 0.3934 0.3841 n_refl.: 13583 remove outliers: r(all,work,free)=0.3925 0.3933 0.3841 n_refl.: 13580 overall B=7.43 to atoms: r(all,work,free)=0.4217 0.4227 0.4091 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.2182 0.2162 0.2544 n_refl.: 13580 remove outliers: r(all,work,free)=0.2181 0.2161 0.2544 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5432 2167.891 1699.946 1.237 1.215 0.394 19.362-15.234 92.45 91 7 0.4008 2001.516 1851.844 0.999 1.207 0.352 15.182-11.849 95.91 195 16 0.2182 2357.622 2247.797 1.016 1.196 0.346 11.824-9.235 95.44 396 23 0.1342 2602.458 2571.289 0.979 1.173 0.344 9.223-7.200 96.44 830 38 0.1832 1876.452 1853.962 0.974 1.135 0.330 7.195-5.615 96.35 1675 92 0.2488 1247.522 1185.861 0.934 1.073 0.276 5.612-4.379 97.24 3486 178 0.1919 1353.373 1301.390 0.987 0.969 0.222 4.378-3.502 95.73 6123 328 0.2280 1060.465 1008.484 1.225 0.812 0.131 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0575 b_overall=4.7221 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.297727 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.254008 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 0.2425 0.2672 0.0247 0.003 0.7 12.0 5.0 15.3 0 0.125 0.2409 0.2668 0.0259 0.003 0.7 11.8 5.0 15.6 0 0.250 0.2337 0.2627 0.0290 0.003 0.8 15.3 5.3 16.0 0 0.500 0.2293 0.2616 0.0323 0.004 0.8 15.3 5.3 17.1 0 1.000 0.2213 0.2564 0.0352 0.006 0.9 20.2 5.0 17.5 0 2.000 0.2174 0.2534 0.0360 0.007 1.0 26.1 5.0 18.9 0 3.000 0.2146 0.2512 0.0366 0.009 1.0 27.7 6.0 20.0 0 4.000 0.2123 0.2495 0.0372 0.010 1.1 30.8 6.3 21.5 0 5.000 0.2102 0.2484 0.0382 0.011 1.2 32.2 6.0 22.2 0 6.000 0.2087 0.2477 0.0390 0.012 1.3 33.5 6.9 23.6 0 7.000 0.2068 0.2471 0.0403 0.013 1.4 35.1 7.2 24.4 0 8.000 0.2057 0.2465 0.0408 0.015 1.4 37.1 6.9 24.7 0 9.000 0.2045 0.2467 0.0422 0.015 1.5 37.9 6.9 25.1 0 10.000 0.2055 0.2464 0.0410 0.015 1.4 37.5 7.2 25.1 0 9.149 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2213 0.2564 0.0352 0.006 0.9 20.2 5.0 17.5 0 2.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.13 25.64 3.52 1.196 57.300 0.254 0.061 22.19 25.52 3.33 2.587 57.522 0.008 0.061 21.99 25.42 3.44 2.691 57.595 0.032 0.060 21.47 25.17 3.70 3.140 57.711 0.127 0.058 20.85 24.86 4.01 5.375 58.142 0.254 0.055 20.62 24.78 4.15 6.173 58.307 0.381 0.054 20.41 24.70 4.29 7.201 58.606 0.508 0.053 20.31 24.65 4.34 7.776 58.742 0.635 0.053 20.23 24.62 4.38 8.258 58.861 0.762 0.052 20.17 24.59 4.42 8.716 58.980 0.889 0.052 20.12 24.56 4.44 9.082 59.073 1.016 0.052 20.06 24.52 4.47 9.579 59.215 1.143 0.051 20.02 24.52 4.50 9.868 59.293 1.270 0.051 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 1.270 Accepted refinement result: 20.02 24.52 4.50 9.868 59.293 1.270 0.051 Individual atomic B min max mean iso aniso Overall: 13.61 164.48 61.57 9.09 2531 0 Protein: 13.61 164.48 61.57 9.09 2531 0 Chain A: 13.61 164.48 61.57 N/A 2531 0 Histogram: Values Number of atoms 13.61 - 28.70 161 28.70 - 43.78 624 43.78 - 58.87 613 58.87 - 73.96 505 73.96 - 89.05 263 89.05 - 104.13 126 104.13 - 119.22 65 119.22 - 134.31 67 134.31 - 149.39 77 149.39 - 164.48 30 =========================== Idealize ADP of riding H ========================== r_work=0.2002 r_free=0.2452 r_work=0.1984 r_free=0.2428 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.1984 r_free= 0.2428 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.050422 | | target function (ls_wunit_k1) not normalized (work): 649.894179 | | target function (ls_wunit_k1) not normalized (free): 54.033886 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2007 0.1984 0.2428 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4247 0.4255 0.4154 n_refl.: 13579 remove outliers: r(all,work,free)=0.4247 0.4255 0.4154 n_refl.: 13579 overall B=0.00 to atoms: r(all,work,free)=0.4247 0.4255 0.4154 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2014 0.1991 0.2441 n_refl.: 13579 remove outliers: r(all,work,free)=0.2014 0.1991 0.2441 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5123 1180.554 966.864 1.112 1.183 0.386 19.362-15.234 92.45 91 7 0.3545 1089.952 1036.328 1.021 1.176 0.354 15.182-11.849 95.91 195 16 0.2000 1283.874 1241.974 1.050 1.167 0.343 11.824-9.235 95.44 396 23 0.1383 1417.203 1403.661 1.013 1.147 0.335 9.223-7.200 96.44 830 38 0.1803 1021.847 1011.808 1.021 1.114 0.330 7.195-5.615 96.35 1675 92 0.2317 679.355 649.060 0.970 1.059 0.280 5.612-4.379 97.24 3486 178 0.1736 736.997 714.500 1.001 0.968 0.210 4.378-3.502 95.73 6123 328 0.2067 577.490 552.697 1.229 0.829 0.119 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.3710 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.373304 wxc_scale = 0.045 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.057211 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 0.2199 0.2541 0.0342 0.003 0.7 11.0 4.4 16.0 0 0.020 0.2148 0.2510 0.0362 0.003 0.7 10.6 4.1 16.7 0 0.059 0.2129 0.2469 0.0340 0.003 0.7 10.6 4.4 17.1 0 0.117 0.2075 0.2439 0.0364 0.003 0.7 11.8 3.8 17.5 0 0.176 0.2048 0.2415 0.0367 0.003 0.7 12.6 3.8 17.8 0 0.234 0.2019 0.2394 0.0375 0.004 0.7 14.5 3.8 18.2 0 0.293 0.2003 0.2383 0.0380 0.004 0.7 15.7 3.8 18.5 0 0.351 0.1989 0.2370 0.0381 0.005 0.8 16.5 3.8 18.9 0 0.410 0.2062 0.2432 0.0370 0.003 0.7 12.2 3.8 18.2 0 0.195 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2148 0.2510 0.0362 0.003 0.7 10.6 4.1 16.7 0 0.059 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.48 25.10 3.62 11.670 68.374 0.057 6.637 23.63 25.95 2.32 11.444 71.667 0.002 6.688 23.09 25.54 2.45 11.608 70.452 0.007 6.672 21.95 24.89 2.94 12.166 68.405 0.029 6.633 21.53 24.76 3.24 12.587 68.152 0.057 6.617 21.30 24.70 3.40 12.946 68.292 0.086 6.609 21.15 24.70 3.56 13.319 68.467 0.114 6.604 21.05 24.69 3.65 13.684 68.641 0.143 6.600 20.97 24.69 3.72 14.050 68.805 0.172 6.598 20.92 24.68 3.76 14.407 68.973 0.200 6.595 20.87 24.68 3.81 14.759 69.121 0.229 6.594 20.84 24.69 3.85 15.022 69.212 0.257 6.593 20.81 24.68 3.87 15.347 69.342 0.286 6.592 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.200 Accepted refinement result: 20.92 24.68 3.76 14.407 68.973 0.200 6.595 Individual atomic B min max mean iso aniso Overall: 11.71 172.65 62.77 14.29 2531 0 Protein: 11.71 172.65 62.77 14.29 2531 0 Chain A: 11.71 172.65 62.77 N/A 2531 0 Histogram: Values Number of atoms 11.71 - 27.80 138 27.80 - 43.90 683 43.90 - 59.99 664 59.99 - 76.09 412 76.09 - 92.18 226 92.18 - 108.27 135 108.27 - 124.37 94 124.37 - 140.46 82 140.46 - 156.55 68 156.55 - 172.65 29 =========================== Idealize ADP of riding H ========================== r_work=0.2092 r_free=0.2468 r_work=0.2094 r_free=0.2472 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2094 r_free= 0.2472 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.593355 | | target function (ml) not normalized (work): 84981.751345 | | target function (ml) not normalized (free): 4616.080756 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2113 0.2094 0.2472 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4228 0.4237 0.4105 n_refl.: 13579 remove outliers: r(all,work,free)=0.4228 0.4237 0.4105 n_refl.: 13579 overall B=1.34 to atoms: r(all,work,free)=0.4284 0.4294 0.4154 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2106 0.2086 0.2465 n_refl.: 13579 remove outliers: r(all,work,free)=0.2106 0.2086 0.2465 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5089 1180.554 955.041 1.242 1.163 0.400 19.362-15.234 92.45 91 7 0.3687 1089.952 1029.335 1.021 1.157 0.349 15.182-11.849 95.91 195 16 0.2121 1283.874 1240.006 1.104 1.150 0.346 11.824-9.235 95.44 396 23 0.1496 1417.203 1402.098 1.062 1.131 0.338 9.223-7.200 96.44 830 38 0.2086 1021.847 1005.314 1.053 1.102 0.328 7.195-5.615 96.35 1675 92 0.2577 679.355 640.431 1.009 1.052 0.278 5.612-4.379 97.24 3486 178 0.1901 736.997 708.029 1.003 0.969 0.217 4.378-3.502 95.73 6123 328 0.2012 577.490 549.445 1.198 0.842 0.112 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.0517 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2086 r_free=0.2465 After: r_work=0.2086 r_free=0.2466 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.477950 wxc_scale = 0.028 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.054423 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 0.2089 0.2468 0.0379 0.003 0.7 11.4 4.4 16.4 0 0.013 0.2088 0.2467 0.0380 0.003 0.7 11.2 4.4 16.4 0 0.038 0.2087 0.2467 0.0380 0.003 0.7 11.2 4.4 16.4 0 0.076 0.2086 0.2465 0.0379 0.003 0.7 11.2 4.4 16.4 0 0.115 0.2086 0.2464 0.0378 0.003 0.7 11.2 4.4 16.4 0 0.153 0.2085 0.2464 0.0380 0.003 0.7 11.2 4.4 16.4 0 0.191 0.2083 0.2462 0.0380 0.003 0.7 11.2 4.4 16.4 0 0.229 0.2081 0.2461 0.0380 0.003 0.7 11.0 4.4 16.4 0 0.267 0.2086 0.2465 0.0379 0.003 0.7 11.2 4.4 16.4 0 0.127 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2081 0.2461 0.0380 0.003 0.7 11.0 4.4 16.4 0 0.267 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.81 24.61 3.80 14.244 70.979 0.054 6.594 23.80 26.13 2.33 12.731 75.694 0.002 6.675 23.07 25.61 2.54 12.648 74.184 0.007 6.659 21.74 24.89 3.15 13.482 71.373 0.027 6.621 21.12 24.61 3.50 14.146 70.304 0.054 6.601 20.91 24.55 3.64 14.519 70.076 0.082 6.594 20.77 24.48 3.72 14.707 70.163 0.109 6.590 20.70 24.48 3.78 14.949 70.139 0.136 6.588 20.64 24.46 3.81 15.170 70.122 0.163 6.586 20.60 24.49 3.88 15.329 70.160 0.190 6.585 20.55 24.40 3.86 15.589 70.161 0.218 6.582 20.51 24.39 3.88 15.762 70.211 0.245 6.581 20.54 24.47 3.93 15.837 70.119 0.272 6.583 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.245 Accepted refinement result: 20.51 24.39 3.88 15.762 70.211 0.245 6.581 Individual atomic B min max mean iso aniso Overall: 9.46 181.68 62.57 16.15 2531 0 Protein: 9.46 181.68 62.57 16.15 2531 0 Chain A: 9.46 181.68 62.57 N/A 2531 0 Histogram: Values Number of atoms 9.46 - 26.68 149 26.68 - 43.90 699 43.90 - 61.12 718 61.12 - 78.35 364 78.35 - 95.57 213 95.57 - 112.79 138 112.79 - 130.01 89 130.01 - 147.23 76 147.23 - 164.46 62 164.46 - 181.68 23 =========================== Idealize ADP of riding H ========================== r_work=0.2051 r_free=0.2439 r_work=0.2048 r_free=0.2438 ----------X-ray data---------- |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2048 r_free= 0.2438 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 6.579630 | | target function (ml) not normalized (work): 84804.853669 | | target function (ml) not normalized (free): 4610.950558 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 55.69 - 5.99 0.96 2723 155 0.2291 0.2630 7.027 7.1263| | 2: 5.98 - 4.75 0.97 2600 136 0.2118 0.2274 6.6672 6.7129| | 3: 4.75 - 4.15 0.98 2607 127 0.1663 0.2249 6.5066 6.6428| | 4: 4.15 - 3.77 0.95 2474 131 0.1883 0.2233 6.3933 6.5057| | 5: 3.77 - 3.50 0.96 2485 141 0.2228 0.2721 6.2598 6.3655| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 55.69 - 5.99 2723 155 0.80 25.15 1.01 0.89 201159.34| | 2: 5.98 - 4.75 2600 136 0.80 26.33 1.00 0.90 138716.35| | 3: 4.75 - 4.15 2607 127 0.87 19.67 0.99 0.89 92641.36| | 4: 4.15 - 3.77 2474 131 0.87 20.08 1.00 0.88 62674.44| | 5: 3.77 - 3.50 2485 141 0.85 22.21 0.96 0.85 48938.91| |alpha: min = 0.85 max = 0.90 mean = 0.88| |beta: min = 48938.91 max = 201159.34 mean = 110683.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.95 mean = 22.74| |phase err.(test): min = 0.00 max = 89.71 mean = 22.58| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2068 0.2048 0.2438 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4186 0.4196 0.4060 n_refl.: 13579 remove outliers: r(all,work,free)=0.4186 0.4196 0.4060 n_refl.: 13579 overall B=1.29 to atoms: r(all,work,free)=0.4240 0.4250 0.4107 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2078 0.2057 0.2450 n_refl.: 13579 remove outliers: r(all,work,free)=0.2078 0.2057 0.2450 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5128 1180.554 956.439 1.310 1.113 0.400 19.362-15.234 92.45 91 7 0.3689 1089.952 1031.624 1.066 1.110 0.347 15.182-11.849 95.91 195 16 0.2130 1283.874 1243.235 1.150 1.106 0.342 11.824-9.235 95.44 396 23 0.1505 1417.203 1405.880 1.113 1.092 0.339 9.223-7.200 96.44 830 38 0.2084 1021.847 1007.077 1.101 1.072 0.338 7.195-5.615 96.35 1675 92 0.2575 679.355 640.862 1.034 1.035 0.278 5.612-4.379 97.24 3486 178 0.1868 736.997 707.593 0.994 0.975 0.217 4.378-3.502 95.73 6123 328 0.1957 577.490 549.951 1.145 0.883 0.104 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.7893 ================= 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 : 0.3934 0.3841 0.010 1.670 9.3 143.2 50.1 0 0.000 1_bss: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_settarget: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_weight: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_xyzrec: 0.2213 0.2564 0.006 0.865 16.8 150.6 57.6 0 0.225 1_adp: 0.2002 0.2452 0.006 0.865 13.6 164.5 61.6 0 0.225 1_regHadp: 0.1984 0.2428 0.006 0.865 13.6 164.5 61.6 0 0.225 2_bss: 0.1991 0.2441 0.006 0.865 13.6 164.5 61.6 0 0.225 2_settarget: 0.1991 0.2441 0.006 0.865 13.6 164.5 61.6 0 0.225 2_updatecdl: 0.1991 0.2441 0.006 0.909 13.6 164.5 61.6 0 0.225 2_weight: 0.1991 0.2441 0.006 0.909 13.6 164.5 61.6 0 0.225 2_xyzrec: 0.2148 0.2510 0.003 0.674 13.6 164.5 61.6 0 0.284 2_adp: 0.2092 0.2468 0.003 0.674 11.7 172.6 62.8 0 0.284 2_regHadp: 0.2094 0.2472 0.003 0.674 11.7 172.6 62.8 0 0.284 3_bss: 0.2086 0.2465 0.003 0.674 13.1 174.0 64.1 0 0.284 3_settarget: 0.2086 0.2465 0.003 0.674 13.1 174.0 64.1 0 0.284 3_updatecdl: 0.2086 0.2465 0.003 0.711 13.1 174.0 64.1 0 0.284 3_setrh: 0.2086 0.2466 0.003 0.711 13.1 174.0 64.1 0 0.283 3_weight: 0.2086 0.2466 0.003 0.711 13.1 174.0 64.1 0 0.283 3_xyzrec: 0.2081 0.2461 0.003 0.689 13.1 174.0 64.1 0 0.283 3_adp: 0.2051 0.2439 0.003 0.689 9.5 181.7 62.6 0 0.283 3_regHadp: 0.2048 0.2438 0.003 0.689 9.5 181.7 62.6 0 0.283 end: 0.2057 0.2450 0.003 0.689 10.7 183.0 63.9 0 0.283 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1fb5_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1fb5_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.8200 Refinement macro-cycles (run) : 279.9200 Write final files (write_after_run_outputs) : 17.1600 Total : 304.9000 Total CPU time: 5.76 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:58 PDT -0700 (1716251758.57 s) Start R-work = 0.2161, R-free = 0.2544 Final R-work = 0.2057, R-free = 0.2450 =============================================================================== Job complete usr+sys time: 367.58 seconds wall clock time: 18 minutes 48.24 seconds (1128.24 seconds total)