Starting qr.refine on Sun May 19 14:03:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5yi5_6830.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5yi5_6830.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 { real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5yi5_6830.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5yi5_6830.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5yi5_6830.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5yi5_6830.pdb" } 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 133": "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: 2774 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2774 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Time building chain proxies: 0.40, per 1000 atoms: 0.14 Number of scatterers: 2774 At special positions: 0 Unit cell: (72.66, 62.879, 58.687, 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 7 16.00 O 273 8.00 N 248 7.00 C 886 6.00 H 1360 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: 0.43 Adding C-beta torsion restraints... Number of C-beta restraints generated: 330 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 1357 1.14 - 1.31: 253 1.31 - 1.48: 567 1.48 - 1.64: 615 1.64 - 1.81: 11 Bond restraints: 2803 Sorted by residual: bond pdb=" C GLN A 59 " pdb=" O GLN A 59 " ideal model delta sigma weight residual 1.231 1.247 -0.016 2.00e-02 2.50e+03 6.14e-01 bond pdb=" C ILE A 25 " pdb=" N ASN A 26 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.14e-01 bond pdb=" C LEU A 107 " pdb=" O LEU A 107 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 5.05e-01 bond pdb=" C ILE A 21 " pdb=" N ASN A 22 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 4.82e-01 bond pdb=" C GLU A 62 " pdb=" N GLU A 63 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 4.61e-01 ... (remaining 2798 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.64: 31 106.64 - 113.47: 3234 113.47 - 120.29: 950 120.29 - 127.12: 814 127.12 - 133.95: 15 Bond angle restraints: 5044 Sorted by residual: angle pdb=" N LEU A 49 " pdb=" CA LEU A 49 " pdb=" C LEU A 49 " ideal model delta sigma weight residual 111.00 106.32 4.68 2.80e+00 1.28e-01 2.79e+00 angle pdb=" CA ASP A 127 " pdb=" C ASP A 127 " pdb=" N PRO A 128 " ideal model delta sigma weight residual 116.90 119.40 -2.50 1.50e+00 4.44e-01 2.78e+00 angle pdb=" C GLU A 62 " pdb=" N GLU A 63 " pdb=" CA GLU A 63 " ideal model delta sigma weight residual 121.70 118.70 3.00 1.80e+00 3.09e-01 2.78e+00 angle pdb=" C TYR A 40 " pdb=" N TYR A 41 " pdb=" CA TYR A 41 " ideal model delta sigma weight residual 121.70 118.72 2.98 1.80e+00 3.09e-01 2.74e+00 angle pdb=" CA HIS A 137 " pdb=" C HIS A 137 " pdb=" N TYR A 138 " ideal model delta sigma weight residual 116.20 119.50 -3.30 2.00e+00 2.50e-01 2.73e+00 ... (remaining 5039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 1261 16.31 - 32.63: 34 32.63 - 48.94: 8 48.94 - 65.25: 8 65.25 - 81.56: 4 Dihedral angle restraints: 1315 sinusoidal: 703 harmonic: 612 Sorted by residual: dihedral pdb=" CA THR A 136 " pdb=" C THR A 136 " pdb=" N HIS A 137 " pdb=" CA HIS A 137 " ideal model delta harmonic sigma weight residual -180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TRP A 94 " pdb=" C TRP A 94 " pdb=" N GLU A 95 " pdb=" CA GLU A 95 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA LEU A 49 " pdb=" C LEU A 49 " pdb=" N LYS A 50 " pdb=" CA LYS A 50 " ideal model delta harmonic sigma weight residual -180.00 -165.42 -14.58 0 5.00e+00 4.00e-02 8.51e+00 ... (remaining 1312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 130 0.024 - 0.047: 52 0.047 - 0.071: 15 0.071 - 0.095: 4 0.095 - 0.118: 3 Chirality restraints: 204 Sorted by residual: chirality pdb=" CA ILE A 86 " pdb=" N ILE A 86 " pdb=" C ILE A 86 " pdb=" CB ILE A 86 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA VAL A 47 " pdb=" N VAL A 47 " pdb=" C VAL A 47 " pdb=" CB VAL A 47 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.88e-01 chirality pdb=" CA ILE A 81 " pdb=" N ILE A 81 " pdb=" C ILE A 81 " pdb=" CB ILE A 81 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 2.81e-01 ... (remaining 201 not shown) Planarity restraints: 425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 17 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C SER A 17 " 0.021 2.00e-02 2.50e+03 pdb=" O SER A 17 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU A 18 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 151 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.04e+00 pdb=" C ASP A 151 " 0.018 2.00e-02 2.50e+03 pdb=" O ASP A 151 " -0.007 2.00e-02 2.50e+03 pdb=" N HIS A 152 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 21 " -0.005 2.00e-02 2.50e+03 9.26e-03 8.57e-01 pdb=" C ILE A 21 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE A 21 " -0.006 2.00e-02 2.50e+03 pdb=" N ASN A 22 " -0.005 2.00e-02 2.50e+03 ... (remaining 422 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 214 2.19 - 2.79: 5162 2.79 - 3.39: 7152 3.39 - 4.00: 8889 4.00 - 4.60: 13480 Nonbonded interactions: 34897 Sorted by model distance: nonbonded pdb=" HH TYR A 41 " pdb=" OD1 ASP A 93 " model vdw 1.583 1.800 nonbonded pdb=" O HIS A 106 " pdb="HD22 ASN A 110 " model vdw 1.633 1.800 nonbonded pdb=" O GLY A 79 " pdb="HH11 ARG A 80 " model vdw 1.662 1.800 nonbonded pdb=" OE1 GLU A 163 " pdb=" H GLU A 163 " model vdw 1.670 1.800 nonbonded pdb=" HH TYR A 35 " pdb=" OE2 GLU A 108 " model vdw 1.678 1.800 ... (remaining 34892 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 7 15.96 2 O 273 7.97 2 N 248 6.97 2 C 886 5.97 2 H 1360 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 1443 Z= 0.217 ANGLE : 0.858 6.143 1944 Z= 0.426 CHIRALITY : 0.031 0.118 204 PLANARITY : 0.003 0.016 257 DIHEDRAL : 10.142 81.563 543 MIN NONBONDED DISTANCE : 2.150 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.72 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 5.29 % FAVORED : 94.71 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.00 % FAVORED : 100.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 33.33 % 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: -0.39 (0.57), RESIDUES: 170 HELIX: 0.04 (0.40), RESIDUES: 126 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -0.74 (0.90), RESIDUES: 44 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.000 ARG A 64 TYR 0.004 0.001 TYR A 169 PHE 0.005 0.001 PHE A 52 TRP 0.005 0.001 TRP A 94 HIS 0.003 0.001 HIS A 129 Resolution of map is: 3.9738 Map-model correlation coefficient (CC) CC_mask : 0.7930 weight= None bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 Initial weight estimate from ratio of grad norms: 0.5153451208687415 cycle: 0 start: weight= 0.5153 bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.5153 bond: 0.026 angle: 3.05 clash: 29.6 rota: 2.61 rama: f: 84.12 o: 1.76 Z: -5.82 cb: 1.21 shift=0.5585 cc_mask=0.8380 cycle: 1 start: weight= 0.3607 bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.3607 bond: 0.021 angle: 2.58 clash: 19.5 rota: 0.65 rama: f: 88.24 o: 0.59 Z: -4.75 cb: 0.00 shift=0.5056 cc_mask=0.8337 cycle: 2 start: weight= 0.2525 bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.2525 bond: 0.017 angle: 2.21 clash: 10.5 rota: 0.65 rama: f: 92.35 o: 0.59 Z: -3.57 cb: 0.00 shift=0.4389 cc_mask=0.8292 cycle: 3 start: weight= 0.1263 bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.1263 bond: 0.012 angle: 1.72 clash: 2.5 rota: 0.00 rama: f: 96.47 o: 0.00 Z: -1.95 cb: 0.00 shift=0.3183 cc_mask=0.8173 cycle: 4 start: weight= 0.0884 bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.0884 bond: 0.011 angle: 1.58 clash: 1.4 rota: 0.00 rama: f: 97.65 o: 0.00 Z: -1.17 cb: 0.00 shift=0.2731 cc_mask=0.8128 cycle: 5 start: weight= 0.0619 bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.0619 bond: 0.010 angle: 1.50 clash: 1.1 rota: 0.00 rama: f: 98.24 o: 0.00 Z: -0.27 cb: 0.00 shift=0.2389 cc_mask=0.8078 cycle: 6 start: weight= 0.0309 bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.0309 bond: 0.009 angle: 1.42 clash: 0.7 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.34 cb: 0.00 shift=0.2106 cc_mask=0.8003 cycle: 7 start: weight= 0.0217 bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.0217 bond: 0.009 angle: 1.41 clash: 0.4 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.55 cb: 0.00 shift=0.2036 cc_mask=0.7984 cycle: 8 start: weight= 0.0152 bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.0152 bond: 0.009 angle: 1.39 clash: 0.4 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.61 cb: 0.00 shift=0.2013 cc_mask=0.7967 cycle: 9 start: weight= 0.0076 bond: 0.004 angle: 0.86 clash: 0.7 rota: 0.00 rama: f: 94.71 o: 0.00 Z: -0.39 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.0076 bond: 0.009 angle: 1.39 clash: 0.4 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.67 cb: 0.00 shift=0.2066 cc_mask=0.7941 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.007578729765635822 start: weight= 0.0076 bond: 0.009 angle: 1.39 clash: 0.4 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.67 cb: 0.00 shift=0.0000 cc_mask=0.7930 final: weight= 0.0076 bond: 0.009 angle: 1.38 clash: 0.4 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.72 cb: 0.00 shift=0.2014 cc_mask=0.7943 start: weight= 0.0076 bond: 0.009 angle: 1.38 clash: 0.4 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.72 cb: 0.00 shift=0.2014 cc_mask=0.7943 final: weight= 0.0076 bond: 0.009 angle: 1.38 clash: 0.7 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.18 cb: 0.00 shift=0.3168 cc_mask=0.7889 start: weight= 0.0076 bond: 0.009 angle: 1.38 clash: 0.7 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.18 cb: 0.00 shift=0.3168 cc_mask=0.7889 final: weight= 0.0076 bond: 0.009 angle: 1.37 clash: 0.7 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.12 cb: 0.00 shift=0.4068 cc_mask=0.7827 start: weight= 0.0076 bond: 0.009 angle: 1.37 clash: 0.7 rota: 0.00 rama: f: 98.24 o: 0.00 Z: 0.12 cb: 0.00 shift=0.4068 cc_mask=0.7827 final: weight= 0.0076 bond: 0.009 angle: 1.38 clash: 0.4 rota: 0.00 rama: f: 97.65 o: 0.00 Z: 0.19 cb: 0.00 shift=0.4732 cc_mask=0.7768 start: weight= 0.0076 bond: 0.009 angle: 1.38 clash: 0.4 rota: 0.00 rama: f: 97.65 o: 0.00 Z: 0.19 cb: 0.00 shift=0.4732 cc_mask=0.7768 final: weight= 0.0076 bond: 0.009 angle: 1.38 clash: 0.4 rota: 0.00 rama: f: 97.65 o: 0.00 Z: 0.13 cb: 0.00 shift=0.5186 cc_mask=0.7714 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.032 1443 Z= 0.487 ANGLE : 1.381 9.396 1944 Z= 0.799 CHIRALITY : 0.099 0.342 204 PLANARITY : 0.019 0.192 257 DIHEDRAL : 12.704 87.441 543 MIN NONBONDED DISTANCE : 2.526 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.36 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.35 % FAVORED : 97.65 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.00 % FAVORED : 100.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 33.33 % 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: 0.13 (0.57), RESIDUES: 170 HELIX: 0.35 (0.39), RESIDUES: 129 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -0.37 (1.02), RESIDUES: 41 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.014 0.005 ARG A 77 TYR 0.069 0.016 TYR A 40 PHE 0.035 0.014 PHE A 133 TRP 0.024 0.013 TRP A 94 HIS 0.009 0.002 HIS A 152 Resolution of map is: 3.9738 Map-model correlation coefficient (CC) CC_mask : 0.7714 =============================================================================== Job complete usr+sys time: 280.54 seconds wall clock time: 5 minutes 18.88 seconds (318.88 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)