Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_1x24.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1x24/1x24.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 amber.topology_file_name=4amber_1x24.prmtop amber.coordinate_file_name=4amber_1x24.rst7 amber.order_file_name=4amber_1x24.order use_amber=True strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Processing files from PHIL: ------------------------------------------------------------------------------- Files not used by program: -------------------------- 4amber_1x24.prmtop 4amber_1x24.rst7 4amber_1x24.order Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "4phenix_1x24.pdb" } default_model = "4phenix_1x24.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1x24/1x24.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1x24/1x24.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } amber { use_amber = True topology_file_name = 4amber_1x24.prmtop coordinate_file_name = 4amber_1x24.rst7 order_file_name = 4amber_1x24.order } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/bootstrap/modules/chem_data/mon_lib" Total number of atoms: 4960 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2480 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain: "B" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2480 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Time building chain proxies: 0.64, per 1000 atoms: 0.13 Number of scatterers: 4960 At special positions: 0 Unit cell: (146.891, 146.891, 146.891, 90, 90, 90) Space group: I 21 3 (No. 199) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 434 8.00 N 424 7.00 C 1580 6.00 H 2508 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 104 " distance=2.01 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 104 " distance=2.02 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: 0.91 Conformation dependent library (CDL) restraints added in 115.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 2 sheets defined 42.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.847A pdb=" N GLU A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 94 removed outlier: 3.865A pdb=" N PHE A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.616A pdb=" N VAL A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 137 removed outlier: 4.210A pdb=" N LYS A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.721A pdb=" N GLU B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.830A pdb=" N PHE B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.642A pdb=" N VAL B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 4.186A pdb=" N LYS B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 151 Processing sheet with id= A, first strand: chain 'A' and resid 10 through 14 removed outlier: 6.401A pdb=" N ILE A 100 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR A 22 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 102 " --> pdb=" O THR A 22 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA A 101 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE A 45 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N HIS A 103 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ARG A 47 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS A 64 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG A 47 " --> pdb=" O HIS A 64 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 66 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.440A pdb=" N ILE B 100 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR B 22 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 102 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA B 101 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 45 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N HIS B 103 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG B 47 " --> pdb=" O HIS B 103 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS B 64 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG B 47 " --> pdb=" O HIS B 64 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 66 " --> pdb=" O ARG B 47 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 237 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: 0.97 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2504 1.15 - 1.32: 456 1.32 - 1.50: 982 1.50 - 1.67: 1052 1.67 - 1.84: 20 Bond restraints: 5014 Sorted by residual: bond pdb=" N ILE A 45 " pdb=" H ILE A 45 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE ARG A 153 " pdb=" HE ARG A 153 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND2 ASN B 24 " pdb="HD22 ASN B 24 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN A 145 " pdb="HE21 GLN A 145 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ILE A 80 " pdb=" H ILE A 80 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 5009 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.19: 382 107.19 - 113.90: 5754 113.90 - 120.62: 1661 120.62 - 127.33: 1290 127.33 - 134.05: 19 Bond angle restraints: 9106 Sorted by residual: angle pdb=" N ARG B 93 " pdb=" CA ARG B 93 " pdb=" C ARG B 93 " ideal model delta sigma weight residual 111.40 103.59 7.81 1.22e+00 6.72e-01 4.10e+01 angle pdb=" C GLU B 95 " pdb=" N PRO B 96 " pdb=" CA PRO B 96 " ideal model delta sigma weight residual 119.84 127.73 -7.89 1.25e+00 6.40e-01 3.99e+01 angle pdb=" N ARG A 93 " pdb=" CA ARG A 93 " pdb=" C ARG A 93 " ideal model delta sigma weight residual 111.40 103.82 7.58 1.22e+00 6.72e-01 3.86e+01 angle pdb=" C GLU A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta sigma weight residual 119.84 127.01 -7.17 1.25e+00 6.40e-01 3.29e+01 angle pdb=" N LYS A 91 " pdb=" CA LYS A 91 " pdb=" C LYS A 91 " ideal model delta sigma weight residual 110.80 120.32 -9.52 2.13e+00 2.20e-01 2.00e+01 ... (remaining 9101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 2051 15.13 - 30.26: 163 30.26 - 45.39: 74 45.39 - 60.52: 46 60.52 - 75.65: 6 Dihedral angle restraints: 2340 sinusoidal: 1294 harmonic: 1046 Sorted by residual: dihedral pdb=" CB CYS B 49 " pdb=" SG CYS B 49 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual 93.00 59.98 33.02 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" N LEU A 158 " pdb=" CA LEU A 158 " pdb=" CB LEU A 158 " pdb=" CG LEU A 158 " ideal model delta sinusoidal sigma weight residual -60.00 -117.55 57.55 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N VAL B 12 " pdb=" CA VAL B 12 " pdb=" CB VAL B 12 " pdb=" CG1 VAL B 12 " ideal model delta sinusoidal sigma weight residual 60.00 3.29 56.71 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2337 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.065: 177 0.065 - 0.129: 129 0.129 - 0.193: 56 0.193 - 0.257: 12 0.257 - 0.322: 6 Chirality restraints: 380 Sorted by residual: chirality pdb=" CA LYS A 91 " pdb=" N LYS A 91 " pdb=" C LYS A 91 " pdb=" CB LYS A 91 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA ILE B 100 " pdb=" N ILE B 100 " pdb=" C ILE B 100 " pdb=" CB ILE B 100 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA LYS B 91 " pdb=" N LYS B 91 " pdb=" C LYS B 91 " pdb=" CB LYS B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 377 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 14 " -0.055 2.00e-02 2.50e+03 2.08e-02 1.30e+01 pdb=" CG TYR B 14 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 14 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 14 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 14 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 14 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 14 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 14 " -0.028 2.00e-02 2.50e+03 pdb=" HD1 TYR B 14 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR B 14 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR B 14 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR B 14 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 14 " 0.053 2.00e-02 2.50e+03 2.01e-02 1.21e+01 pdb=" CG TYR A 14 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 14 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 14 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 14 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 14 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 14 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 14 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR A 14 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR A 14 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 TYR A 14 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 14 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 70 " 0.053 2.00e-02 2.50e+03 1.97e-02 1.16e+01 pdb=" CG PHE B 70 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE B 70 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 70 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 70 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 70 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE B 70 " -0.023 2.00e-02 2.50e+03 pdb=" HD2 PHE B 70 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 PHE B 70 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE B 70 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 70 " 0.019 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 0.59 - 1.39: 9 1.39 - 2.20: 624 2.20 - 3.00: 14160 3.00 - 3.80: 22987 3.80 - 4.60: 36594 Warning: very small nonbonded interaction distances. Nonbonded interactions: 74374 Sorted by model distance: nonbonded pdb=" HH TYR A 53 " pdb=" HE2 HIS A 103 " model vdw 0.592 2.100 nonbonded pdb=" HH TYR B 53 " pdb=" HE2 HIS B 103 " model vdw 0.610 2.100 nonbonded pdb=" HB3 CYS B 104 " pdb=" H VAL B 105 " model vdw 1.099 2.270 nonbonded pdb=" HG1 THR B 26 " pdb=" H THR B 29 " model vdw 1.139 2.100 nonbonded pdb=" HG1 THR A 26 " pdb=" H THR A 29 " model vdw 1.149 2.100 ... (remaining 74369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_1x24.prmtop atom order : 4amber_1x24.order coordinates : 4amber_1x24.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 14 15.96 2 O 434 7.97 1 N 424 6.97 1 C 1580 5.97 2 H 2508 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: 2508 of 4960 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4960 n_use_u_iso = 4960 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 = 4960 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4960 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4960 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 30 through 39 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 56 through 61 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 79 through 94 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 111 through 121 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 126 through 137 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 143 through 151 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 30 through 39 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 55 through 61 helix_type = alpha pi *3_10 unknown } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 79 through 94 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 111 through 121 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'B' and resid 126 through 137 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'B' and resid 143 through 151 } sheet { first_strand = chain 'A' and resid 10 through 14 sheet_id = " A" strand { selection = chain 'A' and resid 17 through 22 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 21 and name N bond_start_previous = chain 'A' and resid 10 and name O } strand { selection = chain 'A' and resid 99 through 103 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 100 and name N bond_start_previous = chain 'A' and resid 20 and name O } strand { selection = chain 'A' and resid 42 through 47 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 43 and name N bond_start_previous = chain 'A' and resid 99 and name O } strand { selection = chain 'A' and resid 64 through 66 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 64 and name N bond_start_previous = chain 'A' and resid 45 and name O } } sheet { first_strand = chain 'B' and resid 10 through 14 sheet_id = " B" strand { selection = chain 'B' and resid 17 through 22 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 21 and name N bond_start_previous = chain 'B' and resid 10 and name O } strand { selection = chain 'B' and resid 99 through 103 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 100 and name N bond_start_previous = chain 'B' and resid 20 and name O } strand { selection = chain 'B' and resid 42 through 47 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 43 and name N bond_start_previous = chain 'B' and resid 99 and name O } strand { selection = chain 'B' and resid 64 through 66 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 64 and name N bond_start_previous = chain 'B' and resid 45 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } amber { use_amber = True topology_file_name = "4amber_1x24.prmtop" coordinate_file_name = "4amber_1x24.rst7" order_file_name = "4amber_1x24.order" } } output { prefix = "4phenix_1x24_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== WARNING: failed to analyze molecule topology. Atomic model may be wrong. ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.10 - 25.19 A, n_refl.=9450 (all), 10.31 % free)-------------| | | | r_work= 0.3216 r_free= 0.3514 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 3.705709 | | target function (ml) not normalized (work): 31409.585319 | | target function (ml) not normalized (free): 3716.905992 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.19 - 5.92 0.99 1279 156 0.3984 0.4366 4.573 4.6587| | 2: 5.91 - 4.71 1.00 1245 142 0.2754 0.3059 4.1101 4.2076| | 3: 4.70 - 4.12 1.00 1230 149 0.2991 0.3165 3.9372 3.9738| | 4: 4.11 - 3.74 0.99 1195 141 0.3071 0.3419 3.6257 3.7282| | 5: 3.74 - 3.47 0.99 1236 140 0.2854 0.3013 3.3848 3.5095| | 6: 3.47 - 3.27 0.98 1167 145 0.2751 0.2999 3.1444 3.2259| | 7: 3.27 - 3.10 0.90 1124 101 0.3710 0.4047 3.0382 3.1269| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.19 - 5.92 1279 156 0.60 43.49 0.86 0.02 1482.21| | 2: 5.91 - 4.71 1245 142 0.54 48.67 1.00 0.02 1281.30| | 3: 4.70 - 4.12 1230 149 0.68 37.31 1.29 0.03 685.61| | 4: 4.11 - 3.74 1195 141 0.66 39.37 1.28 0.03 456.55| | 5: 3.74 - 3.47 1236 140 0.73 33.59 1.21 0.03 226.33| | 6: 3.47 - 3.27 1167 145 0.71 34.74 1.11 0.02 133.10| | 7: 3.27 - 3.10 1124 101 0.65 40.73 0.93 0.02 104.35| |alpha: min = 0.02 max = 0.03 mean = 0.02| |beta: min = 104.35 max = 1482.21 mean = 640.89| |figures of merit: min = 0.00 max = 1.00 mean = 0.65| |phase err.(work): min = 0.00 max = 89.98 mean = 39.76| |phase err.(test): min = 0.00 max = 89.44 mean = 39.32| |-----------------------------------------------------------------------------| ----------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 : 0.009 0.077 2506 Z= 0.592 Angle : 1.390 9.518 3390 Z= 0.917 Chirality : 0.099 0.322 380 Planarity : 0.006 0.038 430 Dihedral : 16.447 75.649 948 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 2.67 % Allowed : 8.33 % Favored : 89.00 % Rotamer: Outliers : 7.14 % Allowed : 9.77 % Favored : 83.08 % 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: -4.35 (0.35), residues: 300 helix: -2.77 (0.30), residues: 134 sheet: -1.20 (0.62), residues: 48 loop : -3.64 (0.41), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 18 TYR 0.044 0.013 TYR B 14 PHE 0.031 0.006 PHE B 70 TRP 0.014 0.003 TRP B 68 HIS 0.001 0.001 HIS B 64 Individual atomic B min max mean iso aniso Overall: 3.07 82.07 54.06 7.85 2452 0 Protein: 3.07 82.07 54.06 7.85 2452 0 Chain A: 19.98 82.07 60.93 N/A 1226 0 Chain B: 3.07 82.07 47.19 N/A 1226 0 Histogram: Values Number of atoms 3.07 - 10.97 7 10.97 - 18.87 37 18.87 - 26.77 157 26.77 - 34.67 269 34.67 - 42.57 432 42.57 - 50.47 311 50.47 - 58.37 225 58.37 - 66.27 175 66.27 - 74.17 168 74.17 - 82.07 671 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9450 (all), 10.31 % free)-------------| | | | r_work= 0.3216 r_free= 0.3514 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 3.705709 | | target function (ml) not normalized (work): 31409.585319 | | target function (ml) not normalized (free): 3716.905992 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3247 0.3216 0.3514 n_refl.: 9450 re-set all scales: r(all,work,free)=0.3247 0.3216 0.3514 n_refl.: 9450 remove outliers: r(all,work,free)=0.3236 0.3204 0.3513 n_refl.: 9446 overall B=13.62 to atoms: r(all,work,free)=0.3616 0.3594 0.3811 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2312 0.2273 0.2640 n_refl.: 9446 remove outliers: r(all,work,free)=0.2312 0.2273 0.2640 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.3111 2410.069 2198.324 1.138 1.048 0.371 14.006-11.401 95.00 85 10 0.2521 2702.301 2681.617 1.134 1.044 0.339 11.401-9.290 97.27 153 25 0.1596 3218.700 3140.206 1.128 1.040 0.328 9.217-7.555 99.08 294 28 0.1797 2201.302 2182.649 1.097 1.034 0.315 7.516-6.153 99.14 515 63 0.2345 1435.352 1379.587 0.964 1.024 0.306 6.131-5.015 99.81 954 115 0.2374 1347.252 1283.929 0.874 1.008 0.250 5.003-4.077 99.75 1757 207 0.1905 1481.602 1430.663 1.033 0.985 0.219 4.074-3.318 98.51 3188 384 0.2380 885.348 840.413 1.067 0.949 0.089 3.316-3.104 91.27 1438 130 0.3483 500.290 441.118 0.918 0.920 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0493 b_overall=4.7549 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.261471 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.216708 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2494 0.2759 0.0265 0.014 2.0 0.0 2.7 8.6 0 0.125 0.2351 0.2717 0.0366 0.014 2.1 0.6 3.3 7.1 0 0.250 0.2194 0.2726 0.0531 0.014 2.1 1.4 4.3 7.9 0 0.500 0.2081 0.2700 0.0619 0.016 2.4 4.4 4.0 8.3 0 1.000 0.1974 0.2737 0.0763 0.019 2.9 7.7 4.3 11.7 3 2.000 0.1933 0.2703 0.0770 0.022 3.3 9.5 1.7 9.0 4 3.000 0.1911 0.2690 0.0779 0.025 3.6 10.5 2.3 9.4 7 4.000 0.1988 0.2672 0.0684 0.030 3.3 12.5 2.0 8.3 2 5.000 0.2015 0.2665 0.0650 0.030 2.9 15.5 2.7 8.3 1 6.000 0.2144 0.2650 0.0505 0.023 1.9 20.2 2.7 7.5 0 7.000 0.2082 0.2648 0.0565 0.026 2.2 19.0 2.7 7.5 0 8.000 0.2186 0.2642 0.0457 0.019 1.6 21.0 2.7 7.1 0 9.000 0.2185 0.2642 0.0457 0.020 1.6 21.0 2.7 7.1 0 10.000 0.1967 0.2752 0.0785 0.019 2.9 7.5 3.7 12.0 4 2.131 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2186 0.2642 0.0457 0.019 1.6 21.0 2.7 7.1 0 9.000 0.2185 0.2642 0.0457 0.020 1.6 21.0 2.7 7.1 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.86 26.42 4.57 5.552 67.378 0.217 0.055 22.14 25.80 3.66 6.170 68.285 0.007 0.055 21.87 25.78 3.90 6.087 68.230 0.027 0.054 21.19 25.73 4.54 6.299 68.160 0.108 0.051 20.71 25.64 4.93 6.968 68.198 0.217 0.049 20.45 25.63 5.18 7.587 68.247 0.325 0.048 20.21 25.74 5.53 8.662 68.515 0.433 0.047 20.09 25.76 5.66 9.188 68.590 0.542 0.047 20.00 25.79 5.78 9.636 68.659 0.650 0.046 19.94 25.80 5.86 10.007 68.719 0.758 0.046 19.90 25.82 5.92 10.336 68.775 0.867 0.046 19.86 25.84 5.99 10.654 68.837 0.975 0.046 19.83 25.86 6.03 10.858 68.867 1.084 0.046 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.325 Accepted refinement result: 20.45 25.63 5.18 7.587 68.247 0.325 0.048 Individual atomic B min max mean iso aniso Overall: 16.75 118.11 69.44 7.10 2452 0 Protein: 16.75 118.11 69.44 7.10 2452 0 Chain A: 36.65 118.11 76.36 N/A 1226 0 Chain B: 16.75 116.51 62.53 N/A 1226 0 Histogram: Values Number of atoms 16.75 - 26.89 1 26.89 - 37.02 45 37.02 - 47.16 283 47.16 - 57.30 521 57.30 - 67.43 404 67.43 - 77.57 337 77.57 - 87.71 201 87.71 - 97.84 448 97.84 - 107.98 191 107.98 - 118.11 21 =========================== Idealize ADP of riding H ========================== r_work=0.2045 r_free=0.2563 r_work=0.2027 r_free=0.2551 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2027 r_free= 0.2551 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ls_wunit_k1) (work): 0.047424 | | target function (ls_wunit_k1) not normalized (work): 401.825276 | | target function (ls_wunit_k1) not normalized (free): 74.359071 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2083 0.2027 0.2551 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3592 0.3562 0.3848 n_refl.: 9446 remove outliers: r(all,work,free)=0.3592 0.3562 0.3848 n_refl.: 9446 overall B=1.65 to atoms: r(all,work,free)=0.3654 0.3625 0.3901 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2078 0.2021 0.2554 n_refl.: 9446 remove outliers: r(all,work,free)=0.2078 0.2021 0.2554 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.3077 1505.091 1385.245 1.043 1.039 0.357 14.006-11.401 95.00 85 10 0.2224 1687.590 1693.260 1.060 1.036 0.319 11.401-9.290 97.27 153 25 0.1498 2010.082 1969.555 1.079 1.032 0.319 9.217-7.555 99.08 294 28 0.1562 1374.716 1368.543 1.068 1.025 0.308 7.516-6.153 99.14 515 63 0.2077 896.379 868.802 0.957 1.016 0.297 6.131-5.015 99.81 954 115 0.2077 841.360 813.576 0.892 1.002 0.256 5.003-4.077 99.75 1757 207 0.1579 925.262 905.252 1.045 0.980 0.215 4.074-3.318 98.51 3188 384 0.2174 552.901 531.457 1.104 0.946 0.063 3.316-3.104 91.27 1438 130 0.3242 312.432 281.212 0.984 0.919 0.048 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.3765 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.515679 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049883 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2182 0.2591 0.0409 0.014 2.1 0.8 3.0 8.3 0 0.076 0.1993 0.2564 0.0571 0.014 2.3 2.8 3.3 9.0 1 0.227 0.1893 0.2578 0.0685 0.017 2.7 4.8 4.3 11.7 3 0.455 0.1846 0.2619 0.0773 0.020 3.0 6.1 5.0 14.3 4 0.682 0.1829 0.2601 0.0773 0.022 3.3 8.5 3.0 10.5 5 0.909 0.1817 0.2596 0.0779 0.025 3.8 9.9 2.0 10.2 9 1.137 0.1854 0.2582 0.0728 0.029 3.4 13.1 2.3 9.4 3 1.364 0.1990 0.2560 0.0571 0.024 1.9 20.0 2.7 7.5 0 1.591 0.1845 0.2595 0.0749 0.021 3.2 7.5 4.0 10.5 5 0.758 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1990 0.2560 0.0571 0.024 1.9 20.0 2.7 7.5 0 1.591 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.90 25.60 5.71 11.432 78.344 0.050 6.610 23.81 26.59 2.77 11.567 83.243 0.001 6.658 22.74 25.87 3.13 11.483 82.164 0.006 6.646 21.02 25.59 4.57 11.561 79.367 0.025 6.610 20.25 25.51 5.26 12.000 79.009 0.050 6.594 19.96 25.56 5.60 12.445 79.082 0.075 6.588 19.81 25.61 5.80 12.856 79.239 0.100 6.586 19.63 25.56 5.92 12.911 79.131 0.125 6.583 19.57 25.59 6.02 13.140 79.216 0.150 6.583 19.53 25.62 6.09 13.338 79.294 0.175 6.582 19.51 25.65 6.14 13.405 79.296 0.200 6.583 19.49 25.66 6.17 13.469 79.310 0.224 6.583 19.47 25.69 6.22 13.653 79.401 0.249 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: 0.050 Accepted refinement result: 20.25 25.51 5.26 12.000 79.009 0.050 6.594 Individual atomic B min max mean iso aniso Overall: 25.48 124.16 72.44 7.92 2452 0 Protein: 25.48 124.16 72.44 7.92 2452 0 Chain A: 38.04 124.16 79.75 N/A 1226 0 Chain B: 25.48 123.67 65.13 N/A 1226 0 Histogram: Values Number of atoms 25.48 - 35.35 6 35.35 - 45.21 137 45.21 - 55.08 405 55.08 - 64.95 482 64.95 - 74.82 401 74.82 - 84.69 272 84.69 - 94.55 342 94.55 - 104.42 239 104.42 - 114.29 119 114.29 - 124.16 49 =========================== Idealize ADP of riding H ========================== r_work=0.2025 r_free=0.2551 r_work=0.2035 r_free=0.2553 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2035 r_free= 0.2553 coordinate error (max.-lik. estimate): 0.42 A | | | | normalized target function (ml) (work): 6.593959 | | target function (ml) not normalized (work): 55870.617086 | | target function (ml) not normalized (free): 6601.231164 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2091 0.2035 0.2553 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3722 0.3695 0.3951 n_refl.: 9446 remove outliers: r(all,work,free)=0.3722 0.3695 0.3951 n_refl.: 9446 overall B=0.05 to atoms: r(all,work,free)=0.3725 0.3697 0.3953 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2089 0.2033 0.2556 n_refl.: 9446 remove outliers: r(all,work,free)=0.2089 0.2033 0.2556 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.2994 1505.091 1378.334 1.103 1.024 0.370 14.006-11.401 95.00 85 10 0.2324 1687.590 1688.423 1.093 1.023 0.328 11.401-9.290 97.27 153 25 0.1517 2010.082 1968.878 1.073 1.021 0.313 9.217-7.555 99.08 294 28 0.1593 1374.716 1364.228 1.083 1.017 0.310 7.516-6.153 99.14 515 63 0.2209 896.379 862.091 0.977 1.011 0.300 6.131-5.015 99.81 954 115 0.2220 841.360 805.826 0.910 1.002 0.260 5.003-4.077 99.75 1757 207 0.1662 925.262 896.804 1.055 0.988 0.210 4.074-3.318 98.51 3188 384 0.2087 552.901 527.867 1.103 0.967 0.075 3.316-3.104 91.27 1438 130 0.3015 312.432 281.215 0.967 0.949 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0821 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.505167 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.048737 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2193 0.2578 0.0385 0.014 2.0 0.6 3.7 7.5 1 0.075 0.2000 0.2553 0.0553 0.014 2.3 2.2 3.7 10.5 2 0.226 0.1900 0.2577 0.0677 0.017 2.6 4.2 4.3 12.0 2 0.452 0.1858 0.2572 0.0714 0.020 3.0 5.4 5.0 13.2 3 0.677 0.1953 0.2563 0.0610 0.021 2.6 11.7 2.0 8.6 0 0.903 0.1866 0.2583 0.0717 0.026 3.3 11.3 1.7 10.2 4 1.129 0.1946 0.2566 0.0620 0.025 2.6 15.1 2.3 8.6 0 1.355 0.1908 0.2555 0.0647 0.028 2.9 15.5 2.3 8.6 1 1.580 0.1843 0.2593 0.0750 0.021 3.1 7.3 5.0 13.2 5 0.753 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2000 0.2553 0.0553 0.014 2.3 2.2 3.7 10.5 2 0.226 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.00 25.53 5.53 12.033 79.969 0.049 6.577 22.94 25.96 3.02 10.950 85.516 0.001 6.635 21.81 25.40 3.60 11.061 84.360 0.006 6.622 19.94 24.97 5.03 11.498 81.347 0.024 6.578 19.18 24.96 5.78 12.178 81.087 0.049 6.556 19.00 25.08 6.08 12.629 80.664 0.073 6.551 18.83 25.09 6.26 13.136 80.947 0.097 6.547 18.82 25.14 6.32 13.379 80.947 0.122 6.547 18.82 25.19 6.37 13.555 80.979 0.146 6.547 18.80 25.22 6.42 13.743 81.060 0.171 6.547 18.78 25.25 6.47 13.932 81.160 0.195 6.547 18.77 25.28 6.51 14.102 81.249 0.219 6.548 18.76 25.29 6.53 14.257 81.329 0.244 6.548 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.049 Accepted refinement result: 19.18 24.96 5.78 12.178 81.087 0.049 6.556 Individual atomic B min max mean iso aniso Overall: 33.25 144.75 74.76 8.83 2452 0 Protein: 33.25 144.75 74.76 8.83 2452 0 Chain A: 39.40 144.75 82.85 N/A 1226 0 Chain B: 33.25 136.47 66.66 N/A 1226 0 Histogram: Values Number of atoms 33.25 - 44.40 89 44.40 - 55.55 400 55.55 - 66.70 537 66.70 - 77.85 451 77.85 - 89.00 348 89.00 - 100.15 279 100.15 - 111.30 192 111.30 - 122.45 107 122.45 - 133.60 41 133.60 - 144.75 8 =========================== Idealize ADP of riding H ========================== r_work=0.1918 r_free=0.2496 r_work=0.1917 r_free=0.2497 ----------X-ray data---------- |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.1917 r_free= 0.2497 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.555969 | | target function (ml) not normalized (work): 55548.725561 | | target function (ml) not normalized (free): 6569.788368 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.19 - 5.92 0.99 1276 155 0.1926 0.2526 7.1077 7.3872| | 2: 5.91 - 4.71 1.00 1245 142 0.1874 0.2381 6.8885 7.0435| | 3: 4.70 - 4.12 1.00 1230 149 0.1541 0.2055 6.7325 6.8751| | 4: 4.11 - 3.74 0.99 1195 141 0.1933 0.2426 6.5525 6.7081| | 5: 3.74 - 3.47 0.99 1236 140 0.1819 0.2621 6.3481 6.5537| | 6: 3.47 - 3.27 0.98 1167 145 0.2275 0.3134 6.143 6.3137| | 7: 3.27 - 3.10 0.90 1124 101 0.2953 0.3498 6.0291 6.152| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.19 - 5.92 1276 155 0.80 26.01 1.00 1.03 304626.32| | 2: 5.91 - 4.71 1245 142 0.76 29.83 1.01 1.03 270664.90| | 3: 4.70 - 4.12 1230 149 0.84 23.13 1.00 1.03 169970.35| | 4: 4.11 - 3.74 1195 141 0.79 27.53 1.03 1.01 126829.49| | 5: 3.74 - 3.47 1236 140 0.81 26.48 0.98 0.98 83471.47| | 6: 3.47 - 3.27 1167 145 0.78 28.95 0.92 0.91 54164.81| | 7: 3.27 - 3.10 1124 101 0.69 37.29 0.96 0.89 45129.68| |alpha: min = 0.89 max = 1.03 mean = 0.99| |beta: min = 45129.68 max = 304626.32 mean = 153831.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.78| |phase err.(work): min = 0.00 max = 89.73 mean = 28.34| |phase err.(test): min = 0.00 max = 88.11 mean = 26.96| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1980 0.1917 0.2497 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3731 0.3702 0.3980 n_refl.: 9446 remove outliers: r(all,work,free)=0.3731 0.3702 0.3980 n_refl.: 9446 overall B=0.00 to atoms: r(all,work,free)=0.3731 0.3702 0.3980 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.1978 0.1918 0.2474 n_refl.: 9446 remove outliers: r(all,work,free)=0.1978 0.1918 0.2474 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.2745 1505.091 1390.283 1.142 1.009 0.380 14.006-11.401 95.00 85 10 0.1921 1687.590 1698.512 1.102 1.010 0.340 11.401-9.290 97.27 153 25 0.1370 2010.082 1968.867 1.083 1.009 0.330 9.217-7.555 99.08 294 28 0.1498 1374.716 1368.952 1.077 1.007 0.310 7.516-6.153 99.14 515 63 0.2239 896.379 854.936 0.999 1.005 0.300 6.131-5.015 99.81 954 115 0.2149 841.360 803.810 0.922 1.000 0.270 5.003-4.077 99.75 1757 207 0.1552 925.262 904.902 1.028 0.993 0.220 4.074-3.318 98.51 3188 384 0.1979 552.901 532.402 1.050 0.983 0.061 3.316-3.104 91.27 1438 130 0.2761 312.432 285.194 0.909 0.974 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=2.1851 ================= 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 : 0.3216 0.3514 0.009 1.390 3.1 82.1 54.1 0 0.000 1_bss: 0.2273 0.2640 0.009 1.390 16.7 95.7 67.7 0 0.000 1_settarget: 0.2273 0.2640 0.009 1.390 16.7 95.7 67.7 0 0.000 1_weight: 0.2273 0.2640 0.009 1.390 16.7 95.7 67.7 0 0.000 1_xyzrec: 0.2186 0.2642 0.019 1.609 16.7 95.7 67.7 0 0.015 1_adp: 0.2045 0.2563 0.019 1.609 16.8 118.1 69.4 0 0.015 1_regHadp: 0.2027 0.2551 0.019 1.609 16.8 118.1 69.4 0 0.015 2_bss: 0.2021 0.2554 0.019 1.609 18.4 119.8 71.1 0 0.015 2_settarget: 0.2021 0.2554 0.019 1.609 18.4 119.8 71.1 0 0.015 2_updatecdl: 0.2021 0.2554 0.019 1.610 18.4 119.8 71.1 0 0.015 2_weight: 0.2021 0.2554 0.019 1.610 18.4 119.8 71.1 0 0.015 2_xyzrec: 0.1990 0.2560 0.024 1.865 18.4 119.8 71.1 0 0.023 2_adp: 0.2025 0.2551 0.024 1.865 25.5 124.2 72.4 0 0.023 2_regHadp: 0.2035 0.2553 0.024 1.865 25.5 124.2 72.4 0 0.023 3_bss: 0.2033 0.2556 0.024 1.865 25.5 124.2 72.5 0 0.023 3_settarget: 0.2033 0.2556 0.024 1.865 25.5 124.2 72.5 0 0.023 3_updatecdl: 0.2033 0.2556 0.024 1.861 25.5 124.2 72.5 0 0.023 3_setrh: 0.2033 0.2556 0.024 1.861 25.5 124.2 72.5 0 0.023 3_weight: 0.2033 0.2556 0.024 1.861 25.5 124.2 72.5 0 0.023 3_xyzrec: 0.2000 0.2553 0.014 2.278 25.5 124.2 72.5 0 0.313 3_adp: 0.1918 0.2496 0.014 2.278 33.2 144.8 74.8 0 0.313 3_regHadp: 0.1917 0.2497 0.014 2.278 33.2 144.8 74.8 0 0.313 end: 0.1918 0.2474 0.014 2.278 33.2 144.8 74.8 0 0.313 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1x24_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1x24_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9300 Refinement macro-cycles (run) : 413.0700 Write final files (write_after_run_outputs) : 11.0400 Total : 427.0400 Total CPU time: 8.22 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:51:13 PDT -0700 (1723222273.93 s) Start R-work = 0.2273, R-free = 0.2640 Final R-work = 0.1918, R-free = 0.2474 =============================================================================== Job complete usr+sys time: 503.78 seconds wall clock time: 19 minutes 47.68 seconds (1187.68 seconds total)