Starting qr.refine on Sun May 19 15:07:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi2_43246.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi2_43246.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/8vi2_43246.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi2_43246.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi2_43246.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8vi2_43246.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 PHE 260": "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: 4943 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4943 Classifications: {'peptide': 308} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 13, 'TRANS': 294} Time building chain proxies: 0.62, per 1000 atoms: 0.13 Number of scatterers: 4943 At special positions: 0 Unit cell: (56.6, 55.468, 63.392, 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 2490 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: 0.98 Adding C-beta torsion restraints... Number of C-beta restraints generated: 568 Time building geometry restraints manager: 1.11 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: 2489 1.14 - 1.31: 356 1.31 - 1.47: 1106 1.47 - 1.64: 1056 1.64 - 1.80: 17 Bond restraints: 5024 Sorted by residual: bond pdb=" C PHE A 7 " pdb=" N PRO A 8 " ideal model delta sigma weight residual 1.341 1.355 -0.014 1.60e-02 3.91e+03 7.90e-01 bond pdb=" C VAL A 47 " pdb=" N ALA A 48 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.28e-01 bond pdb=" C ILE A 86 " pdb=" O ILE A 86 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 4.61e-01 bond pdb=" C ASN A 101 " pdb=" O ASN A 101 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 4.60e-01 bond pdb=" C ALA A 206 " pdb=" O ALA A 206 " ideal model delta sigma weight residual 1.231 1.244 -0.013 2.00e-02 2.50e+03 4.37e-01 ... (remaining 5019 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.32: 194 107.32 - 113.99: 5685 113.99 - 120.65: 1992 120.65 - 127.32: 1173 127.32 - 133.98: 38 Bond angle restraints: 9082 Sorted by residual: angle pdb=" C SER A 192 " pdb=" CA SER A 192 " pdb=" CB SER A 192 " ideal model delta sigma weight residual 110.10 115.87 -5.77 1.90e+00 2.77e-01 9.22e+00 angle pdb=" CA GLU A 181 " pdb=" C GLU A 181 " pdb=" N PRO A 182 " ideal model delta sigma weight residual 116.90 121.34 -4.44 1.50e+00 4.44e-01 8.77e+00 angle pdb=" CA PHE A 245 " pdb=" C PHE A 245 " pdb=" N PRO A 246 " ideal model delta sigma weight residual 116.90 121.20 -4.30 1.50e+00 4.44e-01 8.22e+00 angle pdb=" CA ILE A 86 " pdb=" C ILE A 86 " pdb=" N PRO A 87 " ideal model delta sigma weight residual 116.90 121.11 -4.21 1.50e+00 4.44e-01 7.87e+00 angle pdb=" CA LEU A 144 " pdb=" C LEU A 144 " pdb=" N PRO A 145 " ideal model delta sigma weight residual 116.90 121.06 -4.16 1.50e+00 4.44e-01 7.69e+00 ... (remaining 9077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 2189 16.33 - 32.65: 113 32.65 - 48.98: 50 48.98 - 65.30: 24 65.30 - 81.63: 2 Dihedral angle restraints: 2378 sinusoidal: 1211 harmonic: 1167 Sorted by residual: dihedral pdb=" CB MET A 294 " pdb=" CG MET A 294 " pdb=" SD MET A 294 " pdb=" CE MET A 294 " ideal model delta sinusoidal sigma weight residual 180.00 125.69 54.31 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CB LYS A 251 " pdb=" CG LYS A 251 " pdb=" CD LYS A 251 " pdb=" CE LYS A 251 " ideal model delta sinusoidal sigma weight residual 180.00 127.03 52.97 3 1.50e+01 4.44e-03 9.16e+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 -107.94 47.94 3 1.50e+01 4.44e-03 8.57e+00 ... (remaining 2375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 233 0.024 - 0.048: 97 0.048 - 0.072: 33 0.072 - 0.096: 20 0.096 - 0.120: 7 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA PRO A 8 " pdb=" N PRO A 8 " pdb=" C PRO A 8 " pdb=" CB PRO A 8 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.61e-01 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 3.17e-01 chirality pdb=" CA VAL A 223 " pdb=" N VAL A 223 " pdb=" C VAL A 223 " pdb=" CB VAL A 223 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 387 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 9 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 10 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 10 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 10 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 7 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 8 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 8 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 8 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 144 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.66e-01 pdb=" N PRO A 145 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " -0.014 5.00e-02 4.00e+02 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 342 2.08 - 2.71: 7385 2.71 - 3.34: 15624 3.34 - 3.97: 20442 3.97 - 4.60: 30037 Nonbonded interactions: 73830 Sorted by model distance: nonbonded pdb=" HH TYR A 13 " pdb=" O PHE A 311 " model vdw 1.447 1.800 nonbonded pdb=" O SER A 261 " pdb=" H ALA A 265 " model vdw 1.487 1.800 nonbonded pdb=" O ASN A 269 " pdb=" HG1 THR A 272 " model vdw 1.518 1.800 nonbonded pdb=" O VAL A 212 " pdb=" H LEU A 216 " model vdw 1.531 1.800 nonbonded pdb=" O THR A 121 " pdb=" HG SER A 125 " model vdw 1.553 1.800 ... (remaining 73825 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 2490 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= 0.199 ANGLE : 0.897 5.769 3457 Z= 0.454 CHIRALITY : 0.036 0.120 390 PLANARITY : 0.004 0.029 420 DIHEDRAL : 11.751 81.625 856 MIN NONBONDED DISTANCE : 2.293 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.01 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 3.59 % FAVORED : 96.41 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 1.57 % 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: 0.10 (0.50), RESIDUES: 306 HELIX: 0.10 (0.34), RESIDUES: 239 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 0.53 (0.89), RESIDUES: 67 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.001 0.000 ARG A 198 TYR 0.006 0.001 TYR A 233 PHE 0.010 0.001 PHE A 197 TRP 0.007 0.001 TRP A 231 HIS 0.001 0.000 HIS A 163 Resolution of map is: 3.3765 Map-model correlation coefficient (CC) CC_mask : 0.8523 weight= None bond: 0.004 angle: 0.90 clash: 1.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: 0.10 cb: 0.00 shift=0.0000 cc_mask=0.8523 Initial weight estimate from ratio of grad norms: 0.29483605119914164 cycle: 0 start: weight= 0.2948 bond: 0.004 angle: 0.90 clash: 1.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: 0.10 cb: 0.00 shift=0.0000 cc_mask=0.8523 final: weight= 0.2948 bond: 0.022 angle: 1.98 clash: 2.0 rota: 0.00 rama: f: 96.73 o: 0.00 Z: -4.70 cb: 0.35 shift=0.3138 cc_mask=0.8860 cycle: 1 start: weight= 0.2064 bond: 0.004 angle: 0.90 clash: 1.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: 0.10 cb: 0.00 shift=0.0000 cc_mask=0.8523 final: weight= 0.2064 bond: 0.017 angle: 1.73 clash: 1.2 rota: 0.00 rama: f: 97.71 o: 0.00 Z: -3.62 cb: 0.00 shift=0.2840 cc_mask=0.8823 cycle: 2 start: weight= 0.1445 bond: 0.004 angle: 0.90 clash: 1.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: 0.10 cb: 0.00 shift=0.0000 cc_mask=0.8523 final: weight= 0.1445 bond: 0.014 angle: 1.56 clash: 0.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -2.74 cb: 0.00 shift=0.2576 cc_mask=0.8785 cycle: 3 start: weight= 0.0722 bond: 0.004 angle: 0.90 clash: 1.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: 0.10 cb: 0.00 shift=0.0000 cc_mask=0.8523 final: weight= 0.0722 bond: 0.011 angle: 1.39 clash: 0.6 rota: 0.00 rama: f: 98.37 o: 0.00 Z: -1.69 cb: 0.00 shift=0.2156 cc_mask=0.8716 cycle: 4 start: weight= 0.0506 bond: 0.004 angle: 0.90 clash: 1.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: 0.10 cb: 0.00 shift=0.0000 cc_mask=0.8523 final: weight= 0.0506 bond: 0.010 angle: 1.35 clash: 0.4 rota: 0.00 rama: f: 98.69 o: 0.00 Z: -1.40 cb: 0.00 shift=0.2022 cc_mask=0.8682 cycle: 5 start: weight= 0.0354 bond: 0.004 angle: 0.90 clash: 1.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: 0.10 cb: 0.00 shift=0.0000 cc_mask=0.8523 final: weight= 0.0354 bond: 0.009 angle: 1.32 clash: 0.4 rota: 0.00 rama: f: 99.02 o: 0.00 Z: -1.17 cb: 0.00 shift=0.1880 cc_mask=0.8651 cycle: 6 start: weight= 0.0177 bond: 0.004 angle: 0.90 clash: 1.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: 0.10 cb: 0.00 shift=0.0000 cc_mask=0.8523 final: weight= 0.0177 bond: 0.009 angle: 1.29 clash: 0.4 rota: 0.00 rama: f: 99.02 o: 0.00 Z: -1.10 cb: 0.00 shift=0.1804 cc_mask=0.8607 cycle: 7 start: weight= 0.0124 bond: 0.004 angle: 0.90 clash: 1.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: 0.10 cb: 0.00 shift=0.0000 cc_mask=0.8523 final: weight= 0.0124 bond: 0.009 angle: 1.29 clash: 0.4 rota: 0.00 rama: f: 99.02 o: 0.00 Z: -1.10 cb: 0.00 shift=0.1798 cc_mask=0.8591 cycle: 8 start: weight= 0.0087 bond: 0.004 angle: 0.90 clash: 1.0 rota: 0.00 rama: f: 96.41 o: 0.00 Z: 0.10 cb: 0.00 shift=0.0000 cc_mask=0.8523 final: weight= 0.0087 bond: 0.009 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 99.02 o: 0.00 Z: -1.12 cb: 0.00 shift=0.1796 cc_mask=0.8579 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.008671791646881956 start: weight= 0.0087 bond: 0.009 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 99.02 o: 0.00 Z: -1.12 cb: 0.00 shift=0.0000 cc_mask=0.8523 final: weight= 0.0087 bond: 0.009 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 99.02 o: 0.00 Z: -1.09 cb: 0.00 shift=0.1779 cc_mask=0.8579 start: weight= 0.0087 bond: 0.009 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 99.02 o: 0.00 Z: -1.09 cb: 0.00 shift=0.1779 cc_mask=0.8579 final: weight= 0.0087 bond: 0.008 angle: 1.28 clash: 0.0 rota: 0.00 rama: f: 98.37 o: 0.00 Z: -1.15 cb: 0.35 shift=0.2374 cc_mask=0.8573 start: weight= 0.0087 bond: 0.008 angle: 1.28 clash: 0.0 rota: 0.00 rama: f: 98.37 o: 0.00 Z: -1.15 cb: 0.35 shift=0.2374 cc_mask=0.8573 final: weight= 0.0087 bond: 0.008 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 98.37 o: 0.00 Z: -1.39 cb: 0.00 shift=0.2681 cc_mask=0.8567 start: weight= 0.0087 bond: 0.008 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 98.37 o: 0.00 Z: -1.39 cb: 0.00 shift=0.2681 cc_mask=0.8567 final: weight= 0.0087 bond: 0.008 angle: 1.27 clash: 0.0 rota: 0.00 rama: f: 98.37 o: 0.00 Z: -1.45 cb: 0.00 shift=0.2984 cc_mask=0.8558 start: weight= 0.0087 bond: 0.008 angle: 1.27 clash: 0.0 rota: 0.00 rama: f: 98.37 o: 0.00 Z: -1.45 cb: 0.00 shift=0.2984 cc_mask=0.8558 final: weight= 0.0087 bond: 0.008 angle: 1.28 clash: 0.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -1.45 cb: 0.35 shift=0.3190 cc_mask=0.8546 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.008 0.040 2534 Z= 0.444 ANGLE : 1.281 8.808 3457 Z= 0.681 CHIRALITY : 0.113 0.376 390 PLANARITY : 0.012 0.116 420 DIHEDRAL : 12.000 86.894 856 MIN NONBONDED DISTANCE : 2.634 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.20 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.96 % FAVORED : 98.04 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 1.57 % FAVORED : 98.43 % CBETA DEVIATIONS : 0.35 % 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: -1.45 (0.42), RESIDUES: 306 HELIX: -1.13 (0.25), RESIDUES: 241 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 0.68 (0.95), RESIDUES: 65 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.018 0.004 ARG A 38 TYR 0.099 0.014 TYR A 143 PHE 0.045 0.011 PHE A 151 TRP 0.118 0.017 TRP A 231 HIS 0.006 0.002 HIS A 163 Resolution of map is: 3.3765 Map-model correlation coefficient (CC) CC_mask : 0.8546 =============================================================================== Job complete usr+sys time: 420.68 seconds wall clock time: 7 minutes 41.28 seconds (461.28 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)