Starting qr.refine on Sun May 19 13:49:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8ve0_43160.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8ve0_43160.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/8ve0_43160.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8ve0_43160.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8ve0_43160.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8ve0_43160.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 116": "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: 1791 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1791 Classifications: {'peptide': 117} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Time building chain proxies: 0.30, per 1000 atoms: 0.17 Number of scatterers: 1791 At special positions: 0 Unit cell: (43.274, 56.2, 48.894, 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 176 8.00 N 149 7.00 C 579 6.00 H 885 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: 0.30 Adding C-beta torsion restraints... Number of C-beta restraints generated: 220 Time building geometry restraints manager: 0.35 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: 884 1.14 - 1.31: 152 1.31 - 1.47: 377 1.47 - 1.64: 399 1.64 - 1.80: 3 Bond restraints: 1815 Sorted by residual: bond pdb=" C GLY A 101 " pdb=" N PRO A 102 " ideal model delta sigma weight residual 1.341 1.332 0.009 1.60e-02 3.91e+03 2.94e-01 bond pdb=" C SER A 23 " pdb=" N PRO A 24 " ideal model delta sigma weight residual 1.341 1.332 0.009 1.60e-02 3.91e+03 2.85e-01 bond pdb=" C TYR A 78 " pdb=" O TYR A 78 " ideal model delta sigma weight residual 1.231 1.241 -0.010 2.00e-02 2.50e+03 2.60e-01 bond pdb=" CA ASN A 124 " pdb=" CB ASN A 124 " ideal model delta sigma weight residual 1.530 1.520 0.010 2.00e-02 2.50e+03 2.51e-01 bond pdb=" N GLY A 101 " pdb=" CA GLY A 101 " ideal model delta sigma weight residual 1.451 1.443 0.008 1.60e-02 3.91e+03 2.44e-01 ... (remaining 1810 not shown) Histogram of bond angle deviations from ideal: 100.94 - 107.54: 82 107.54 - 114.14: 2192 114.14 - 120.74: 523 120.74 - 127.34: 472 127.34 - 133.95: 14 Bond angle restraints: 3283 Sorted by residual: angle pdb=" CA ASN A 124 " pdb=" C ASN A 124 " pdb=" N PRO A 125 " ideal model delta sigma weight residual 116.90 119.49 -2.59 1.50e+00 4.44e-01 2.99e+00 angle pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 116.90 119.28 -2.38 1.50e+00 4.44e-01 2.51e+00 angle pdb=" C LEU A 111 " pdb=" N SER A 112 " pdb=" CA SER A 112 " ideal model delta sigma weight residual 121.70 124.26 -2.56 1.80e+00 3.09e-01 2.03e+00 angle pdb=" CA GLU A 42 " pdb=" C GLU A 42 " pdb=" N PRO A 43 " ideal model delta sigma weight residual 116.90 118.89 -1.99 1.50e+00 4.44e-01 1.77e+00 angle pdb=" N VAL A 121 " pdb=" CA VAL A 121 " pdb=" C VAL A 121 " ideal model delta sigma weight residual 111.00 107.39 3.61 2.80e+00 1.28e-01 1.66e+00 ... (remaining 3278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.51: 769 11.51 - 23.01: 39 23.01 - 34.52: 34 34.52 - 46.02: 17 46.02 - 57.53: 7 Dihedral angle restraints: 866 sinusoidal: 456 harmonic: 410 Sorted by residual: dihedral pdb=" CA ASP A 38 " pdb=" CB ASP A 38 " pdb=" CG ASP A 38 " pdb=" OD1 ASP A 38 " ideal model delta sinusoidal sigma weight residual -30.00 -86.42 56.42 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP A 39 " pdb=" CB ASP A 39 " pdb=" CG ASP A 39 " pdb=" OD1 ASP A 39 " ideal model delta sinusoidal sigma weight residual -30.00 -81.89 51.89 1 2.00e+01 2.50e-03 9.19e+00 dihedral pdb=" CB ARG A 34 " pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " pdb=" NE ARG A 34 " ideal model delta sinusoidal sigma weight residual 60.00 103.39 -43.39 3 1.50e+01 4.44e-03 7.80e+00 ... (remaining 863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 79 0.026 - 0.052: 42 0.052 - 0.078: 5 0.078 - 0.105: 4 0.105 - 0.131: 14 Chirality restraints: 144 Sorted by residual: chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE A 107 " pdb=" N ILE A 107 " pdb=" C ILE A 107 " pdb=" CB ILE A 107 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 141 not shown) Planarity restraints: 271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 23 " -0.012 5.00e-02 4.00e+02 1.83e-02 5.36e-01 pdb=" N PRO A 24 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 24 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 24 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 124 " -0.011 5.00e-02 4.00e+02 1.73e-02 4.81e-01 pdb=" N PRO A 125 " 0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 85 " 0.011 5.00e-02 4.00e+02 1.72e-02 4.75e-01 pdb=" N PRO A 86 " -0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 86 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 86 " 0.010 5.00e-02 4.00e+02 ... (remaining 268 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 134 2.18 - 2.79: 3323 2.79 - 3.39: 4463 3.39 - 4.00: 6349 4.00 - 4.60: 9033 Nonbonded interactions: 23302 Sorted by model distance: nonbonded pdb=" O VAL A 65 " pdb=" HH TYR A 69 " model vdw 1.577 1.800 nonbonded pdb=" H ASN A 98 " pdb=" OH TYR A 105 " model vdw 1.593 1.800 nonbonded pdb=" HZ3 LYS A 76 " pdb=" OE1 GLU A 89 " model vdw 1.613 1.800 nonbonded pdb=" O VAL A 28 " pdb=" H THR A 49 " model vdw 1.648 1.800 nonbonded pdb=" O PRO A 102 " pdb="HH11 ARG A 103 " model vdw 1.648 1.800 ... (remaining 23297 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 176 7.97 2 N 149 6.97 2 C 579 5.97 2 H 885 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 : 0.003 0.015 930 Z= 0.167 ANGLE : 0.890 3.610 1269 Z= 0.407 CHIRALITY : 0.047 0.131 144 PLANARITY : 0.004 0.018 162 DIHEDRAL : 11.132 56.419 329 MIN NONBONDED DISTANCE : 2.421 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 2.24 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 0.87 % FAVORED : 99.13 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.00 % FAVORED : 100.00 % 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: 0.96 (0.73), RESIDUES: 115 HELIX: 0.17 (1.66), RESIDUES: 9 SHEET: 1.60 (0.69), RESIDUES: 54 LOOP : -0.32 (0.74), RESIDUES: 52 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.001 ARG A 34 TYR 0.005 0.001 TYR A 105 PHE 0.006 0.001 PHE A 44 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.001 HIS A 31 Resolution of map is: 2.7187 Map-model correlation coefficient (CC) CC_mask : 0.7699 weight= None bond: 0.003 angle: 0.89 clash: 2.2 rota: 0.00 rama: f: 99.13 o: 0.00 Z: 0.96 cb: 0.00 shift=0.0000 cc_mask=0.7699 Initial weight estimate from ratio of grad norms: 0.41796493797458545 cycle: 0 start: weight= 0.4180 bond: 0.003 angle: 0.89 clash: 2.2 rota: 0.00 rama: f: 99.13 o: 0.00 Z: 0.96 cb: 0.00 shift=0.0000 cc_mask=0.7699 final: weight= 0.4180 bond: 0.023 angle: 2.40 clash: 7.8 rota: 2.04 rama: f: 87.83 o: 0.87 Z: -4.49 cb: 0.00 shift=0.3939 cc_mask=0.8118 cycle: 1 start: weight= 0.2926 bond: 0.003 angle: 0.89 clash: 2.2 rota: 0.00 rama: f: 99.13 o: 0.00 Z: 0.96 cb: 0.00 shift=0.0000 cc_mask=0.7699 final: weight= 0.2926 bond: 0.018 angle: 2.09 clash: 4.5 rota: 1.02 rama: f: 93.04 o: 0.87 Z: -3.61 cb: 0.00 shift=0.3467 cc_mask=0.8058 cycle: 2 start: weight= 0.2048 bond: 0.003 angle: 0.89 clash: 2.2 rota: 0.00 rama: f: 99.13 o: 0.00 Z: 0.96 cb: 0.00 shift=0.0000 cc_mask=0.7699 final: weight= 0.2048 bond: 0.015 angle: 1.88 clash: 1.7 rota: 0.00 rama: f: 96.52 o: 0.87 Z: -2.65 cb: 0.00 shift=0.3046 cc_mask=0.7998 cycle: 3 start: weight= 0.1024 bond: 0.003 angle: 0.89 clash: 2.2 rota: 0.00 rama: f: 99.13 o: 0.00 Z: 0.96 cb: 0.00 shift=0.0000 cc_mask=0.7699 final: weight= 0.1024 bond: 0.012 angle: 1.66 clash: 0.6 rota: 0.00 rama: f: 97.39 o: 0.00 Z: -1.36 cb: 0.00 shift=0.2394 cc_mask=0.7881 cycle: 4 start: weight= 0.0717 bond: 0.003 angle: 0.89 clash: 2.2 rota: 0.00 rama: f: 99.13 o: 0.00 Z: 0.96 cb: 0.00 shift=0.0000 cc_mask=0.7699 final: weight= 0.0717 bond: 0.011 angle: 1.62 clash: 0.6 rota: 0.00 rama: f: 99.13 o: 0.00 Z: -0.86 cb: 0.00 shift=0.2188 cc_mask=0.7832 cycle: 5 start: weight= 0.0502 bond: 0.003 angle: 0.89 clash: 2.2 rota: 0.00 rama: f: 99.13 o: 0.00 Z: 0.96 cb: 0.00 shift=0.0000 cc_mask=0.7699 final: weight= 0.0502 bond: 0.010 angle: 1.60 clash: 1.1 rota: 0.00 rama: f: 98.26 o: 0.00 Z: -0.44 cb: 0.00 shift=0.2095 cc_mask=0.7791 cycle: 6 start: weight= 0.0251 bond: 0.003 angle: 0.89 clash: 2.2 rota: 0.00 rama: f: 99.13 o: 0.00 Z: 0.96 cb: 0.00 shift=0.0000 cc_mask=0.7699 final: weight= 0.0251 bond: 0.010 angle: 1.59 clash: 1.1 rota: 0.00 rama: f: 98.26 o: 0.00 Z: -0.16 cb: 0.00 shift=0.1957 cc_mask=0.7727 cycle: 7 start: weight= 0.0176 bond: 0.003 angle: 0.89 clash: 2.2 rota: 0.00 rama: f: 99.13 o: 0.00 Z: 0.96 cb: 0.00 shift=0.0000 cc_mask=0.7699 final: weight= 0.0176 bond: 0.010 angle: 1.59 clash: 1.1 rota: 0.00 rama: f: 98.26 o: 0.00 Z: -0.07 cb: 0.00 shift=0.1958 cc_mask=0.7701 cycle: 8 start: weight= 0.0123 bond: 0.003 angle: 0.89 clash: 2.2 rota: 0.00 rama: f: 99.13 o: 0.00 Z: 0.96 cb: 0.00 shift=0.0000 cc_mask=0.7699 final: weight= 0.0123 bond: 0.010 angle: 1.59 clash: 1.1 rota: 0.00 rama: f: 98.26 o: 0.00 Z: -0.05 cb: 0.00 shift=0.1950 cc_mask=0.7685 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.012293289246943003 start: weight= 0.0123 bond: 0.010 angle: 1.59 clash: 1.1 rota: 0.00 rama: f: 98.26 o: 0.00 Z: -0.05 cb: 0.00 shift=0.0000 cc_mask=0.7699 final: weight= 0.0123 bond: 0.010 angle: 1.59 clash: 1.1 rota: 0.00 rama: f: 98.26 o: 0.00 Z: -0.03 cb: 0.00 shift=0.1922 cc_mask=0.7686 start: weight= 0.0123 bond: 0.010 angle: 1.59 clash: 1.1 rota: 0.00 rama: f: 98.26 o: 0.00 Z: -0.03 cb: 0.00 shift=0.1922 cc_mask=0.7686 final: weight= 0.0123 bond: 0.009 angle: 1.57 clash: 1.1 rota: 0.00 rama: f: 99.13 o: 0.00 Z: -0.13 cb: 0.00 shift=0.2596 cc_mask=0.7663 start: weight= 0.0123 bond: 0.009 angle: 1.57 clash: 1.1 rota: 0.00 rama: f: 99.13 o: 0.00 Z: -0.13 cb: 0.00 shift=0.2596 cc_mask=0.7663 final: weight= 0.0123 bond: 0.010 angle: 1.57 clash: 0.0 rota: 0.00 rama: f: 99.13 o: 0.00 Z: -0.31 cb: 0.00 shift=0.3257 cc_mask=0.7629 start: weight= 0.0123 bond: 0.010 angle: 1.57 clash: 0.0 rota: 0.00 rama: f: 99.13 o: 0.00 Z: -0.31 cb: 0.00 shift=0.3257 cc_mask=0.7629 final: weight= 0.0123 bond: 0.010 angle: 1.56 clash: 0.0 rota: 0.00 rama: f: 99.13 o: 0.00 Z: -0.44 cb: 0.00 shift=0.3615 cc_mask=0.7607 start: weight= 0.0123 bond: 0.010 angle: 1.56 clash: 0.0 rota: 0.00 rama: f: 99.13 o: 0.00 Z: -0.44 cb: 0.00 shift=0.3615 cc_mask=0.7607 final: weight= 0.0123 bond: 0.010 angle: 1.56 clash: 0.0 rota: 0.00 rama: f: 99.13 o: 0.00 Z: -0.41 cb: 0.00 shift=0.3982 cc_mask=0.7587 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.010 0.029 930 Z= 0.516 ANGLE : 1.561 8.989 1269 Z= 0.815 CHIRALITY : 0.090 0.289 144 PLANARITY : 0.015 0.105 162 DIHEDRAL : 15.731 115.554 329 MIN NONBONDED DISTANCE : 2.568 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.00 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 0.87 % FAVORED : 99.13 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.00 % FAVORED : 100.00 % 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: -0.41 (0.73), RESIDUES: 115 HELIX: -2.21 (1.36), RESIDUES: 9 SHEET: 0.33 (0.66), RESIDUES: 59 LOOP : -0.53 (0.80), RESIDUES: 47 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.012 0.004 ARG A 34 TYR 0.087 0.016 TYR A 105 PHE 0.032 0.008 PHE A 64 TRP 0.049 0.021 TRP A 79 HIS 0.003 0.001 HIS A 90 Resolution of map is: 2.7187 Map-model correlation coefficient (CC) CC_mask : 0.7587 =============================================================================== Job complete usr+sys time: 208.45 seconds wall clock time: 4 minutes 1.11 seconds (241.11 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)