Starting qr.refine on Sun May 19 14:08:54 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6ezj_3999.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6ezj_3999.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- mode=refine restraints=qm engine=aimnet2 clustering=false minimizer=lbfgsb max_bond_rmsd=0.0001 gradient_only=false Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6ezj_3999.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6ezj_3999.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6ezj_3999.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6ezj_3999.map" } cluster { clustering = false } quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { max_bond_rmsd = 0.0001 minimizer = lbfgs *lbfgsb } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** max_atoms = 50000 debug_rss = False debug = False scattering_table = wk1995 it1992 *n_gaussian electron neutron use_reduce = True cluster { charge_cutoff = 8 clustering = False charge_embedding = False two_buffers = False maxnum_residues_in_cluster = 15 bcc_threshold = 9 select_within_radius = 10 clustering_method = gnc *bcc altloc_method = average *subtract save_clusters = True bond_with_altloc = True re_calculate_rmsd_tolerance = 0.5 } restraints = cctbx *qm expansion = False quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server basis = Auto charge = None method = Auto memory = None nproc = 1 server_url = "http://127.0.0.1:8000" qm_addon = gcp dftd3 gcp-d3 qm_addon_method = None } refine { dry_run = False sf_algorithm = *direct fft refinement_target_name = *ml ls_wunit_k1 mode = opt *refine gtest number_of_macro_cycles = 1 number_of_weight_search_cycles = 50 number_of_refine_cycles = 5 number_of_micro_cycles = 50 data_weight = None skip_weight_search = False adjust_restraints_weight_scale_value = 2 max_iterations_weight = 50 max_iterations_refine = 50 use_ase_lbfgs = False line_search = True stpmax = 0.2 gradient_only = False refine_sites = True refine_adp = False restraints_weight_scale = 1 shake_sites = False use_convergence_test = True max_bond_rmsd = 0.0001 max_angle_rmsd = 1.7 stop_one_found_first_good_weight = True max_r_work_r_free_gap = 5 r_tolerance = 0.001 rmsd_tolerance = 0.01 opt_log = False pre_opt = False pre_opt_stpmax = 0.1 pre_opt_iter = 10 pre_opt_switch = 2 pre_opt_gconv = 3000 minimizer = lbfgs *lbfgsb shift_evaluation = max *mean } parallel { method = *multiprocessing slurm pbs sge lsf threading nproc = 1 qsub_command = None } output_file_name_prefix = None output_folder_name = "pdb" rst_file = None dump_gradients = None output { filename = None file_name = None prefix = None suffix = None serial = 0 serial_format = "%03d" target_output_format = None *pdb mmcif overwrite = False } ------------------------------------------------------------------------------- Extracting model **************** Symmetric amino acids flipped Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/chem_data/mon_lib" Total number of atoms: 2851 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2851 Classifications: {'peptide': 185} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 179} Time building chain proxies: 0.40, per 1000 atoms: 0.14 Number of scatterers: 2851 At special positions: 0 Unit cell: (62.35, 50.525, 60.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 2 16.00 O 276 8.00 N 265 7.00 C 894 6.00 H 1414 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.14: 1414 1.14 - 1.31: 247 1.31 - 1.47: 588 1.47 - 1.64: 625 1.64 - 1.81: 4 Bond restraints: 2878 Sorted by residual: bond pdb=" C GLY A 165 " pdb=" N LYS A 166 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.40e-02 5.10e+03 2.09e+00 bond pdb=" C LEU A 118 " pdb=" N SER A 119 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.40e-02 5.10e+03 1.41e+00 bond pdb=" CB GLU A 109 " pdb=" CG GLU A 109 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.02e-01 bond pdb=" CG GLU A 144 " pdb=" CD GLU A 144 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.49e-01 bond pdb=" CA ARG A 99 " pdb=" CB ARG A 99 " ideal model delta sigma weight residual 1.530 1.545 -0.015 2.00e-02 2.50e+03 5.58e-01 ... (remaining 2873 not shown) Histogram of bond angle deviations from ideal: 100.94 - 107.01: 62 107.01 - 113.09: 3324 113.09 - 119.16: 571 119.16 - 125.23: 1123 125.23 - 131.31: 106 Bond angle restraints: 5186 Sorted by residual: angle pdb=" C ASN A 98 " pdb=" N ARG A 99 " pdb=" CA ARG A 99 " ideal model delta sigma weight residual 121.70 127.11 -5.41 1.80e+00 3.09e-01 9.04e+00 angle pdb=" CA ARG A 99 " pdb=" C ARG A 99 " pdb=" N PHE A 100 " ideal model delta sigma weight residual 116.20 120.03 -3.83 2.00e+00 2.50e-01 3.67e+00 angle pdb=" C LEU A 107 " pdb=" CA LEU A 107 " pdb=" CB LEU A 107 " ideal model delta sigma weight residual 110.10 113.41 -3.31 1.90e+00 2.77e-01 3.04e+00 angle pdb=" N ASP A 37 " pdb=" CA ASP A 37 " pdb=" C ASP A 37 " ideal model delta sigma weight residual 111.00 106.18 4.82 2.80e+00 1.28e-01 2.96e+00 angle pdb=" CA PRO A 43 " pdb=" C PRO A 43 " pdb=" N PHE A 44 " ideal model delta sigma weight residual 116.20 119.57 -3.37 2.00e+00 2.50e-01 2.85e+00 ... (remaining 5181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 1238 15.01 - 30.02: 62 30.02 - 45.02: 29 45.02 - 60.03: 15 60.03 - 75.04: 2 Dihedral angle restraints: 1346 sinusoidal: 733 harmonic: 613 Sorted by residual: dihedral pdb=" CA PRO A 106 " pdb=" C PRO A 106 " pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ILE A 28 " pdb=" C ILE A 28 " pdb=" N ASN A 29 " pdb=" CA ASN A 29 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU A 109 " pdb=" CB GLU A 109 " pdb=" CG GLU A 109 " pdb=" CD GLU A 109 " ideal model delta sinusoidal sigma weight residual -180.00 -121.53 -58.47 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 107 0.025 - 0.050: 74 0.050 - 0.075: 19 0.075 - 0.099: 11 0.099 - 0.124: 14 Chirality restraints: 225 Sorted by residual: chirality pdb=" CA ILE A 42 " pdb=" N ILE A 42 " pdb=" C ILE A 42 " pdb=" CB ILE A 42 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 160 " pdb=" N ILE A 160 " pdb=" C ILE A 160 " pdb=" CB ILE A 160 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE A 70 " pdb=" N ILE A 70 " pdb=" C ILE A 70 " pdb=" CB ILE A 70 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 222 not shown) Planarity restraints: 441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 105 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A 106 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 168 " -0.005 2.00e-02 2.50e+03 9.68e-03 9.38e-01 pdb=" C SER A 168 " 0.017 2.00e-02 2.50e+03 pdb=" O SER A 168 " -0.006 2.00e-02 2.50e+03 pdb=" N HIS A 169 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 121 " -0.015 5.00e-02 4.00e+02 2.24e-02 7.99e-01 pdb=" N PRO A 122 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.012 5.00e-02 4.00e+02 ... (remaining 438 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 258 2.18 - 2.78: 5401 2.78 - 3.39: 7486 3.39 - 3.99: 10573 3.99 - 4.60: 15217 Nonbonded interactions: 38935 Sorted by model distance: nonbonded pdb=" HG1 THR A 22 " pdb=" OD2 ASP A 78 " model vdw 1.571 1.800 nonbonded pdb=" OD1 ASN A 76 " pdb=" HH TYR A 138 " model vdw 1.593 1.800 nonbonded pdb=" O SER A 119 " pdb=" H ARG A 121 " model vdw 1.600 1.800 nonbonded pdb=" OG1 THR A 132 " pdb=" HG SER A 168 " model vdw 1.619 1.800 nonbonded pdb="HD21 ASN A 76 " pdb=" HD1 PHE A 146 " model vdw 1.700 2.000 ... (remaining 38930 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 2 15.96 2 O 276 7.97 2 N 265 6.97 2 C 894 5.97 2 H 1414 1.00 3 sf(0) = scattering factor at diffraction angle 0. Setting QM defaults Setting QM method to HF Setting QM basis to 6-31g GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.004 0.025 1464 Z= 0.199 ANGLE : 0.973 5.412 1981 Z= 0.458 CHIRALITY : 0.044 0.124 225 PLANARITY : 0.004 0.048 262 DIHEDRAL : 11.089 72.094 532 MIN NONBONDED DISTANCE : 2.319 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 2.81 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 10.93 % FAVORED : 89.07 % ROTAMER: OUTLIERS : 1.30 % ALLOWED : 3.90 % FAVORED : 94.81 % 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: -3.98 (0.51), RESIDUES: 183 HELIX: -2.70 (0.49), RESIDUES: 66 SHEET: -1.01 (0.69), RESIDUES: 51 LOOP : -3.78 (0.57), RESIDUES: 66 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.000 ARG A 121 TYR 0.009 0.002 TYR A 138 PHE 0.005 0.001 PHE A 100 HIS 0.003 0.001 HIS A 145 Resolution of map is: 3.0403 Map-model correlation coefficient (CC) CC_mask : 0.7280 weight= None bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 Initial weight estimate from ratio of grad norms: 0.43286320500923664 cycle: 0 start: weight= 0.4329 bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.4329 bond: 0.021 angle: 2.77 clash: 8.4 rota: 3.25 rama: f: 87.43 o: 2.19 Z: -5.03 cb: 7.74 shift=0.3634 cc_mask=0.7753 cycle: 1 start: weight= 0.3030 bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.3030 bond: 0.017 angle: 2.38 clash: 4.9 rota: 3.25 rama: f: 89.07 o: 2.19 Z: -4.54 cb: 3.57 shift=0.3367 cc_mask=0.7696 cycle: 2 start: weight= 0.2121 bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.2121 bond: 0.014 angle: 2.11 clash: 3.9 rota: 3.25 rama: f: 90.71 o: 1.64 Z: -4.28 cb: 2.38 shift=0.3196 cc_mask=0.7639 cycle: 3 start: weight= 0.1061 bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.1061 bond: 0.011 angle: 1.81 clash: 2.1 rota: 1.30 rama: f: 91.80 o: 0.55 Z: -3.80 cb: 1.79 shift=0.2624 cc_mask=0.7524 cycle: 4 start: weight= 0.0742 bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.0742 bond: 0.010 angle: 1.73 clash: 1.4 rota: 1.30 rama: f: 91.80 o: 0.00 Z: -3.32 cb: 1.19 shift=0.2367 cc_mask=0.7465 cycle: 5 start: weight= 0.0520 bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.0520 bond: 0.010 angle: 1.70 clash: 0.7 rota: 1.30 rama: f: 92.35 o: 0.55 Z: -3.13 cb: 1.19 shift=0.2243 cc_mask=0.7410 cycle: 6 start: weight= 0.0260 bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.0260 bond: 0.009 angle: 1.64 clash: 0.4 rota: 0.65 rama: f: 92.90 o: 0.55 Z: -2.72 cb: 0.60 shift=0.2057 cc_mask=0.7326 cycle: 7 start: weight= 0.0182 bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.0182 bond: 0.009 angle: 1.63 clash: 0.4 rota: 0.65 rama: f: 92.35 o: 0.00 Z: -2.62 cb: 0.60 shift=0.2068 cc_mask=0.7299 cycle: 8 start: weight= 0.0127 bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.0127 bond: 0.009 angle: 1.62 clash: 0.4 rota: 0.65 rama: f: 92.35 o: 0.00 Z: -2.52 cb: 0.00 shift=0.2066 cc_mask=0.7277 cycle: 9 start: weight= 0.0064 bond: 0.004 angle: 0.97 clash: 2.8 rota: 1.30 rama: f: 89.07 o: 0.00 Z: -3.98 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.0064 bond: 0.009 angle: 1.62 clash: 0.4 rota: 0.65 rama: f: 91.80 o: 0.00 Z: -2.46 cb: 0.00 shift=0.2101 cc_mask=0.7245 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.006365740400766462 start: weight= 0.0064 bond: 0.009 angle: 1.62 clash: 0.4 rota: 0.65 rama: f: 91.80 o: 0.00 Z: -2.46 cb: 0.00 shift=0.0000 cc_mask=0.7280 final: weight= 0.0064 bond: 0.009 angle: 1.62 clash: 0.4 rota: 0.65 rama: f: 91.80 o: 0.00 Z: -2.45 cb: 0.00 shift=0.2090 cc_mask=0.7246 start: weight= 0.0064 bond: 0.009 angle: 1.62 clash: 0.4 rota: 0.65 rama: f: 91.80 o: 0.00 Z: -2.45 cb: 0.00 shift=0.2090 cc_mask=0.7246 final: weight= 0.0064 bond: 0.009 angle: 1.63 clash: 0.4 rota: 0.00 rama: f: 92.90 o: 0.55 Z: -2.34 cb: 1.19 shift=0.3031 cc_mask=0.7179 start: weight= 0.0064 bond: 0.009 angle: 1.63 clash: 0.4 rota: 0.00 rama: f: 92.90 o: 0.55 Z: -2.34 cb: 1.19 shift=0.3031 cc_mask=0.7179 final: weight= 0.0064 bond: 0.009 angle: 1.62 clash: 0.7 rota: 0.00 rama: f: 92.90 o: 0.55 Z: -2.44 cb: 0.60 shift=0.3492 cc_mask=0.7135 start: weight= 0.0064 bond: 0.009 angle: 1.62 clash: 0.7 rota: 0.00 rama: f: 92.90 o: 0.55 Z: -2.44 cb: 0.60 shift=0.3492 cc_mask=0.7135 final: weight= 0.0064 bond: 0.009 angle: 1.63 clash: 0.4 rota: 0.00 rama: f: 92.35 o: 0.55 Z: -2.56 cb: 0.60 shift=0.3841 cc_mask=0.7100 start: weight= 0.0064 bond: 0.009 angle: 1.63 clash: 0.4 rota: 0.00 rama: f: 92.35 o: 0.55 Z: -2.56 cb: 0.60 shift=0.3841 cc_mask=0.7100 final: weight= 0.0064 bond: 0.009 angle: 1.62 clash: 0.7 rota: 0.00 rama: f: 91.80 o: 0.55 Z: -2.50 cb: 0.60 shift=0.4159 cc_mask=0.7079 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.030 1464 Z= 0.523 ANGLE : 1.622 9.810 1981 Z= 0.939 CHIRALITY : 0.115 0.499 225 PLANARITY : 0.016 0.157 262 DIHEDRAL : 13.593 106.469 532 MIN NONBONDED DISTANCE : 2.587 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.70 RAMACHANDRAN PLOT: OUTLIERS : 0.55 % ALLOWED : 7.65 % FAVORED : 91.80 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 4.55 % FAVORED : 95.45 % CBETA DEVIATIONS : 0.60 % 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: -2.50 (0.59), RESIDUES: 183 HELIX: -1.25 (0.52), RESIDUES: 65 SHEET: -1.03 (0.75), RESIDUES: 59 LOOP : -2.53 (0.74), RESIDUES: 59 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.019 0.004 ARG A 184 TYR 0.047 0.013 TYR A 123 PHE 0.044 0.014 PHE A 44 HIS 0.004 0.001 HIS A 61 Resolution of map is: 3.0403 Map-model correlation coefficient (CC) CC_mask : 0.7079 =============================================================================== Job complete usr+sys time: 291.44 seconds wall clock time: 5 minutes 29.52 seconds (329.52 seconds total) /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/ase/__init__.py:21: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if LooseVersion(np.__version__) < '1.9': /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. other = LooseVersion(other)