Starting qr.refine on Sun May 19 14:50:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi4_43248.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi4_43248.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/8vi4_43248.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi4_43248.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi4_43248.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi4_43248.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 None 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: 4942 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4942 Classifications: {'peptide': 308} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 13, 'TRANS': 294} Time building chain proxies: 0.61, per 1000 atoms: 0.12 Number of scatterers: 4942 At special positions: 0 Unit cell: (61.694, 58.864, 62.826, 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 9 16.00 O 402 8.00 N 380 7.00 C 1662 6.00 H 2489 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: 0.99 Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Time building geometry restraints manager: 1.14 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: 2488 1.14 - 1.31: 356 1.31 - 1.48: 1110 1.48 - 1.64: 1052 1.64 - 1.81: 17 Bond restraints: 5023 Sorted by residual: bond pdb=" N PRO A 182 " pdb=" CA PRO A 182 " ideal model delta sigma weight residual 1.466 1.477 -0.011 1.50e-02 4.44e+03 5.60e-01 bond pdb=" CA SER A 192 " pdb=" CB SER A 192 " ideal model delta sigma weight residual 1.530 1.515 0.015 2.00e-02 2.50e+03 5.48e-01 bond pdb=" C VAL A 40 " pdb=" N SER A 41 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 4.06e-01 bond pdb=" C LEU A 144 " pdb=" O LEU A 144 " ideal model delta sigma weight residual 1.231 1.243 -0.012 2.00e-02 2.50e+03 3.88e-01 bond pdb=" C GLY A 94 " pdb=" N ASP A 95 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 3.83e-01 ... (remaining 5018 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.23: 157 107.23 - 113.92: 5714 113.92 - 120.61: 1939 120.61 - 127.30: 1232 127.30 - 133.98: 38 Bond angle restraints: 9080 Sorted by residual: angle pdb=" CA PHE A 245 " pdb=" C PHE A 245 " pdb=" N PRO A 246 " ideal model delta sigma weight residual 116.90 121.22 -4.32 1.50e+00 4.44e-01 8.31e+00 angle pdb=" CA GLU A 181 " pdb=" C GLU A 181 " pdb=" N PRO A 182 " ideal model delta sigma weight residual 116.90 121.17 -4.27 1.50e+00 4.44e-01 8.11e+00 angle pdb=" CA LEU A 144 " pdb=" C LEU A 144 " pdb=" N PRO A 145 " ideal model delta sigma weight residual 116.90 121.12 -4.22 1.50e+00 4.44e-01 7.91e+00 angle pdb=" C SER A 192 " pdb=" CA SER A 192 " pdb=" CB SER A 192 " ideal model delta sigma weight residual 110.10 114.49 -4.39 1.90e+00 2.77e-01 5.35e+00 angle pdb=" CA ILE A 86 " pdb=" C ILE A 86 " pdb=" N PRO A 87 " ideal model delta sigma weight residual 116.90 119.80 -2.90 1.50e+00 4.44e-01 3.75e+00 ... (remaining 9075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.24: 2164 14.24 - 28.47: 129 28.47 - 42.71: 40 42.71 - 56.94: 37 56.94 - 71.17: 7 Dihedral angle restraints: 2377 sinusoidal: 1211 harmonic: 1166 Sorted by residual: dihedral pdb=" N TRP A 231 " pdb=" CA TRP A 231 " pdb=" CB TRP A 231 " pdb=" CG TRP A 231 " ideal model delta sinusoidal sigma weight residual -60.00 -109.46 49.46 3 1.50e+01 4.44e-03 8.78e+00 dihedral pdb=" CA GLN A 196 " pdb=" CB GLN A 196 " pdb=" CG GLN A 196 " pdb=" CD GLN A 196 " ideal model delta sinusoidal sigma weight residual -60.00 -107.39 47.39 3 1.50e+01 4.44e-03 8.49e+00 dihedral pdb=" CB GLU A 134 " pdb=" CG GLU A 134 " pdb=" CD GLU A 134 " pdb=" OE1 GLU A 134 " ideal model delta sinusoidal sigma weight residual 0.00 -71.17 71.17 1 3.00e+01 1.11e-03 7.22e+00 ... (remaining 2374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 225 0.022 - 0.044: 93 0.044 - 0.066: 26 0.066 - 0.088: 33 0.088 - 0.109: 13 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA VAL A 279 " pdb=" N VAL A 279 " pdb=" C VAL A 279 " pdb=" CB VAL A 279 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.99e-01 chirality pdb=" CA PRO A 207 " pdb=" N PRO A 207 " pdb=" C PRO A 207 " pdb=" CB PRO A 207 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.84e-01 chirality pdb=" CA PRO A 102 " pdb=" N PRO A 102 " pdb=" C PRO A 102 " pdb=" CB PRO A 102 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.39e-01 ... (remaining 387 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 206 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.22e+00 pdb=" N PRO A 207 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 45 " -0.005 2.00e-02 2.50e+03 9.52e-03 9.07e-01 pdb=" C GLY A 45 " 0.016 2.00e-02 2.50e+03 pdb=" O GLY A 45 " -0.006 2.00e-02 2.50e+03 pdb=" N ILE A 46 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 44 " -0.005 2.00e-02 2.50e+03 9.42e-03 8.87e-01 pdb=" C LEU A 44 " 0.016 2.00e-02 2.50e+03 pdb=" O LEU A 44 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY A 45 " -0.005 2.00e-02 2.50e+03 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 477 2.14 - 2.75: 8748 2.75 - 3.37: 15303 3.37 - 3.98: 20156 3.98 - 4.60: 29950 Nonbonded interactions: 74634 Sorted by model distance: nonbonded pdb=" HH TYR A 13 " pdb=" O PHE A 311 " model vdw 1.523 1.800 nonbonded pdb=" O PHE A 197 " pdb=" HG1 THR A 200 " model vdw 1.568 1.800 nonbonded pdb=" HE1 TRP A 258 " pdb=" OG1 THR A 302 " model vdw 1.574 1.800 nonbonded pdb=" O TRP A 258 " pdb=" HG SER A 261 " model vdw 1.584 1.800 nonbonded pdb=" O PRO A 17 " pdb=" H ALA A 21 " model vdw 1.589 1.800 ... (remaining 74629 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 9 15.96 2 O 402 7.97 2 N 380 6.97 2 C 1662 5.97 2 H 2489 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 0.016 2534 Z= 0.203 ANGLE : 0.883 4.582 3457 Z= 0.439 CHIRALITY : 0.035 0.109 390 PLANARITY : 0.004 0.028 420 DIHEDRAL : 11.297 71.175 856 MIN NONBONDED DISTANCE : 2.189 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 3.04 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 5.56 % FAVORED : 94.44 % ROTAMER: OUTLIERS : 0.78 % ALLOWED : 0.00 % FAVORED : 99.22 % 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: -1.31 (0.49), RESIDUES: 306 HELIX: -0.82 (0.33), RESIDUES: 244 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -0.21 (0.90), RESIDUES: 62 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.000 ARG A 198 TYR 0.009 0.001 TYR A 304 PHE 0.008 0.001 PHE A 34 TRP 0.006 0.001 TRP A 177 HIS 0.001 0.000 HIS A 29 Resolution of map is: 3.2818 Map-model correlation coefficient (CC) CC_mask : 0.8841 weight= None bond: 0.004 angle: 0.88 clash: 3.0 rota: 0.78 rama: f: 94.44 o: 0.00 Z: -1.31 cb: 0.00 shift=0.0000 cc_mask=0.8841 Initial weight estimate from ratio of grad norms: 0.26819821748179773 cycle: 0 start: weight= 0.2682 bond: 0.004 angle: 0.88 clash: 3.0 rota: 0.78 rama: f: 94.44 o: 0.00 Z: -1.31 cb: 0.00 shift=0.0000 cc_mask=0.8841 final: weight= 0.2682 bond: 0.021 angle: 1.96 clash: 2.4 rota: 0.78 rama: f: 97.39 o: 0.65 Z: -5.49 cb: 0.00 shift=0.2874 cc_mask=0.9146 cycle: 1 start: weight= 0.1877 bond: 0.004 angle: 0.88 clash: 3.0 rota: 0.78 rama: f: 94.44 o: 0.00 Z: -1.31 cb: 0.00 shift=0.0000 cc_mask=0.8841 final: weight= 0.1877 bond: 0.017 angle: 1.72 clash: 1.0 rota: 0.78 rama: f: 97.39 o: 0.33 Z: -4.31 cb: 0.00 shift=0.2601 cc_mask=0.9110 cycle: 2 start: weight= 0.1314 bond: 0.004 angle: 0.88 clash: 3.0 rota: 0.78 rama: f: 94.44 o: 0.00 Z: -1.31 cb: 0.00 shift=0.0000 cc_mask=0.8841 final: weight= 0.1314 bond: 0.014 angle: 1.56 clash: 0.4 rota: 0.78 rama: f: 97.71 o: 0.33 Z: -3.21 cb: 0.00 shift=0.2336 cc_mask=0.9076 cycle: 3 start: weight= 0.0657 bond: 0.004 angle: 0.88 clash: 3.0 rota: 0.78 rama: f: 94.44 o: 0.00 Z: -1.31 cb: 0.00 shift=0.0000 cc_mask=0.8841 final: weight= 0.0657 bond: 0.011 angle: 1.39 clash: 0.0 rota: 0.78 rama: f: 98.37 o: 0.00 Z: -1.58 cb: 0.00 shift=0.2000 cc_mask=0.9013 cycle: 4 start: weight= 0.0460 bond: 0.004 angle: 0.88 clash: 3.0 rota: 0.78 rama: f: 94.44 o: 0.00 Z: -1.31 cb: 0.00 shift=0.0000 cc_mask=0.8841 final: weight= 0.0460 bond: 0.010 angle: 1.35 clash: 0.0 rota: 0.78 rama: f: 98.37 o: 0.00 Z: -1.24 cb: 0.00 shift=0.1889 cc_mask=0.8983 cycle: 5 start: weight= 0.0322 bond: 0.004 angle: 0.88 clash: 3.0 rota: 0.78 rama: f: 94.44 o: 0.00 Z: -1.31 cb: 0.00 shift=0.0000 cc_mask=0.8841 final: weight= 0.0322 bond: 0.009 angle: 1.33 clash: 0.0 rota: 0.78 rama: f: 98.37 o: 0.00 Z: -1.08 cb: 0.00 shift=0.1834 cc_mask=0.8958 cycle: 6 start: weight= 0.0161 bond: 0.004 angle: 0.88 clash: 3.0 rota: 0.78 rama: f: 94.44 o: 0.00 Z: -1.31 cb: 0.00 shift=0.0000 cc_mask=0.8841 final: weight= 0.0161 bond: 0.009 angle: 1.31 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -0.92 cb: 0.00 shift=0.1769 cc_mask=0.8918 cycle: 7 start: weight= 0.0113 bond: 0.004 angle: 0.88 clash: 3.0 rota: 0.78 rama: f: 94.44 o: 0.00 Z: -1.31 cb: 0.00 shift=0.0000 cc_mask=0.8841 final: weight= 0.0113 bond: 0.009 angle: 1.30 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -0.94 cb: 0.00 shift=0.1774 cc_mask=0.8904 cycle: 8 start: weight= 0.0079 bond: 0.004 angle: 0.88 clash: 3.0 rota: 0.78 rama: f: 94.44 o: 0.00 Z: -1.31 cb: 0.00 shift=0.0000 cc_mask=0.8841 final: weight= 0.0079 bond: 0.009 angle: 1.30 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -0.95 cb: 0.00 shift=0.1769 cc_mask=0.8895 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.007888313022129004 start: weight= 0.0079 bond: 0.009 angle: 1.30 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -0.95 cb: 0.00 shift=0.0000 cc_mask=0.8841 final: weight= 0.0079 bond: 0.009 angle: 1.30 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -0.99 cb: 0.00 shift=0.1781 cc_mask=0.8895 start: weight= 0.0079 bond: 0.009 angle: 1.30 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -0.99 cb: 0.00 shift=0.1781 cc_mask=0.8895 final: weight= 0.0079 bond: 0.008 angle: 1.27 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -1.55 cb: 0.00 shift=0.2284 cc_mask=0.8884 start: weight= 0.0079 bond: 0.008 angle: 1.27 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -1.55 cb: 0.00 shift=0.2284 cc_mask=0.8884 final: weight= 0.0079 bond: 0.008 angle: 1.28 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -1.62 cb: 0.00 shift=0.2620 cc_mask=0.8867 start: weight= 0.0079 bond: 0.008 angle: 1.28 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -1.62 cb: 0.00 shift=0.2620 cc_mask=0.8867 final: weight= 0.0079 bond: 0.008 angle: 1.28 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -1.76 cb: 0.00 shift=0.2792 cc_mask=0.8859 start: weight= 0.0079 bond: 0.008 angle: 1.28 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -1.76 cb: 0.00 shift=0.2792 cc_mask=0.8859 final: weight= 0.0079 bond: 0.008 angle: 1.28 clash: 0.0 rota: 0.39 rama: f: 98.37 o: 0.00 Z: -1.79 cb: 0.00 shift=0.2902 cc_mask=0.8851 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.008 0.040 2534 Z= 0.449 ANGLE : 1.279 8.861 3457 Z= 0.690 CHIRALITY : 0.107 0.323 390 PLANARITY : 0.013 0.135 420 DIHEDRAL : 11.664 77.512 856 MIN NONBONDED DISTANCE : 2.608 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.00 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.63 % FAVORED : 98.37 % ROTAMER: OUTLIERS : 0.39 % ALLOWED : 1.18 % FAVORED : 98.43 % 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: -1.79 (0.41), RESIDUES: 306 HELIX: -1.23 (0.25), RESIDUES: 251 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 0.16 (1.01), RESIDUES: 55 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.017 0.004 ARG A 189 TYR 0.098 0.016 TYR A 143 PHE 0.058 0.011 PHE A 7 TRP 0.032 0.012 TRP A 100 HIS 0.006 0.002 HIS A 139 Resolution of map is: 3.2818 Map-model correlation coefficient (CC) CC_mask : 0.8851 =============================================================================== Job complete usr+sys time: 430.26 seconds wall clock time: 7 minutes 50.06 seconds (470.06 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)