Starting qr.refine on Sun May 19 13:37:45 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dat_27275.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dat_27275.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/8dat_27275.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dat_27275.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dat_27275.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8dat_27275.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: 1226 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1226 Classifications: {'peptide': 76} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Time building chain proxies: 0.23, per 1000 atoms: 0.19 Number of scatterers: 1226 At special positions: 0 Unit cell: (46.816, 43.624, 42.56, 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 1 16.00 O 120 8.00 N 105 7.00 C 375 6.00 H 625 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: 0.24 Adding C-beta torsion restraints... Number of C-beta restraints generated: 140 Time building geometry restraints manager: 0.27 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: 625 1.14 - 1.31: 107 1.31 - 1.47: 210 1.47 - 1.64: 287 1.64 - 1.80: 2 Bond restraints: 1231 Sorted by residual: bond pdb=" C ILE K 236 " pdb=" N PRO K 237 " ideal model delta sigma weight residual 1.341 1.332 0.009 1.60e-02 3.91e+03 3.23e-01 bond pdb=" C PRO K 238 " pdb=" N ASP K 239 " ideal model delta sigma weight residual 1.329 1.336 -0.007 1.40e-02 5.10e+03 2.78e-01 bond pdb=" C GLU K 218 " pdb=" N SER K 219 " ideal model delta sigma weight residual 1.329 1.336 -0.007 1.40e-02 5.10e+03 2.37e-01 bond pdb=" C PRO K 237 " pdb=" O PRO K 237 " ideal model delta sigma weight residual 1.231 1.241 -0.010 2.00e-02 2.50e+03 2.36e-01 bond pdb=" C ILE K 223 " pdb=" N ASP K 224 " ideal model delta sigma weight residual 1.329 1.336 -0.007 1.40e-02 5.10e+03 2.35e-01 ... (remaining 1226 not shown) Histogram of bond angle deviations from ideal: 101.02 - 107.06: 17 107.06 - 113.11: 1536 113.11 - 119.15: 239 119.15 - 125.19: 439 125.19 - 131.23: 10 Bond angle restraints: 2241 Sorted by residual: angle pdb=" CA ILE K 236 " pdb=" C ILE K 236 " pdb=" N PRO K 237 " ideal model delta sigma weight residual 116.90 119.59 -2.69 1.50e+00 4.44e-01 3.21e+00 angle pdb=" CA GLU K 234 " pdb=" C GLU K 234 " pdb=" N GLY K 235 " ideal model delta sigma weight residual 116.20 119.03 -2.83 2.00e+00 2.50e-01 2.00e+00 angle pdb=" N ARG K 242 " pdb=" CA ARG K 242 " pdb=" C ARG K 242 " ideal model delta sigma weight residual 111.00 107.33 3.67 2.80e+00 1.28e-01 1.72e+00 angle pdb=" O ILE K 236 " pdb=" C ILE K 236 " pdb=" N PRO K 237 " ideal model delta sigma weight residual 123.00 120.90 2.10 1.60e+00 3.91e-01 1.72e+00 angle pdb=" CA GLY K 253 " pdb=" C GLY K 253 " pdb=" N ARG K 254 " ideal model delta sigma weight residual 116.20 118.79 -2.59 2.00e+00 2.50e-01 1.68e+00 ... (remaining 2236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.88: 511 13.88 - 27.76: 31 27.76 - 41.65: 13 41.65 - 55.53: 4 55.53 - 69.41: 3 Dihedral angle restraints: 562 sinusoidal: 329 harmonic: 233 Sorted by residual: dihedral pdb=" N LEU K 215 " pdb=" CA LEU K 215 " pdb=" CB LEU K 215 " pdb=" CG LEU K 215 " ideal model delta sinusoidal sigma weight residual -60.00 -97.18 37.18 3 1.50e+01 4.44e-03 6.48e+00 dihedral pdb=" N MET K 201 " pdb=" CA MET K 201 " pdb=" CB MET K 201 " pdb=" CG MET K 201 " ideal model delta sinusoidal sigma weight residual 60.00 95.58 -35.58 3 1.50e+01 4.44e-03 6.11e+00 dihedral pdb=" CB ARG K 274 " pdb=" CG ARG K 274 " pdb=" CD ARG K 274 " pdb=" NE ARG K 274 " ideal model delta sinusoidal sigma weight residual -60.00 -90.67 30.67 3 1.50e+01 4.44e-03 4.91e+00 ... (remaining 559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 65 0.025 - 0.051: 15 0.051 - 0.076: 8 0.076 - 0.101: 3 0.101 - 0.127: 6 Chirality restraints: 97 Sorted by residual: chirality pdb=" CA ILE K 236 " pdb=" N ILE K 236 " pdb=" C ILE K 236 " pdb=" CB ILE K 236 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA VAL K 270 " pdb=" N VAL K 270 " pdb=" C VAL K 270 " pdb=" CB VAL K 270 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CA ILE K 244 " pdb=" N ILE K 244 " pdb=" C ILE K 244 " pdb=" CB ILE K 244 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 94 not shown) Planarity restraints: 178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 236 " 0.009 5.00e-02 4.00e+02 1.41e-02 3.20e-01 pdb=" N PRO K 237 " -0.024 5.00e-02 4.00e+02 pdb=" CA PRO K 237 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO K 237 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 237 " 0.006 5.00e-02 4.00e+02 8.87e-03 1.26e-01 pdb=" N PRO K 238 " -0.015 5.00e-02 4.00e+02 pdb=" CA PRO K 238 " 0.004 5.00e-02 4.00e+02 pdb=" CD PRO K 238 " 0.005 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 204 " -0.003 2.00e-02 2.50e+03 1.82e-03 9.97e-02 pdb=" CG PHE K 204 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE K 204 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE K 204 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE K 204 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE K 204 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE K 204 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE K 204 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE K 204 " -0.001 2.00e-02 2.50e+03 ... (remaining 175 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 148 2.18 - 2.78: 2535 2.78 - 3.39: 3417 3.39 - 3.99: 4574 3.99 - 4.60: 6701 Nonbonded interactions: 17375 Sorted by model distance: nonbonded pdb=" HZ3 LYS K 206 " pdb=" OG1 THR K 212 " model vdw 1.573 1.800 nonbonded pdb=" O GLN K 231 " pdb=" H GLY K 235 " model vdw 1.600 1.800 nonbonded pdb=" OE1 GLU K 218 " pdb=" H GLU K 218 " model vdw 1.638 1.800 nonbonded pdb=" OD1 ASP K 239 " pdb=" H GLN K 240 " model vdw 1.649 1.800 nonbonded pdb=" H ILE K 223 " pdb=" O ARG K 254 " model vdw 1.660 1.800 ... (remaining 17370 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 1 15.96 2 O 120 7.97 2 N 105 6.97 2 C 375 5.97 2 H 625 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 0.012 606 Z= 0.164 ANGLE : 0.858 3.840 814 Z= 0.402 CHIRALITY : 0.042 0.127 97 PLANARITY : 0.002 0.014 105 DIHEDRAL : 10.908 69.410 239 MIN NONBONDED DISTANCE : 2.120 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 9.81 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.05 % FAVORED : 95.95 % ROTAMER: OUTLIERS : 1.45 % ALLOWED : 8.70 % FAVORED : 89.86 % 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: -0.74 (0.96), RESIDUES: 74 HELIX: 0.35 (1.39), RESIDUES: 12 SHEET: -2.29 (0.78), RESIDUES: 25 LOOP : 0.88 (1.12), RESIDUES: 37 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.001 ARG K 272 TYR 0.002 0.001 TYR K 259 PHE 0.005 0.001 PHE K 204 HIS 0.001 0.000 HIS K 268 Resolution of map is: 3.8196 Map-model correlation coefficient (CC) CC_mask : 0.7101 weight= None bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 Initial weight estimate from ratio of grad norms: 0.8981076776359631 cycle: 0 start: weight= 0.8981 bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.8981 bond: 0.027 angle: 3.70 clash: 125.1 rota: 14.49 rama: f: 72.97 o: 5.41 Z: -6.79 cb: 11.43 shift=0.7271 cc_mask=0.7915 cycle: 1 start: weight= 0.6287 bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.6287 bond: 0.021 angle: 3.04 clash: 72.8 rota: 11.59 rama: f: 81.08 o: 4.05 Z: -6.07 cb: 4.29 shift=0.6020 cc_mask=0.7768 cycle: 2 start: weight= 0.4401 bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.4401 bond: 0.017 angle: 2.60 clash: 40.9 rota: 11.59 rama: f: 85.14 o: 0.00 Z: -4.93 cb: 1.43 shift=0.4894 cc_mask=0.7638 cycle: 3 start: weight= 0.2200 bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.2200 bond: 0.013 angle: 2.03 clash: 11.4 rota: 5.80 rama: f: 95.95 o: 0.00 Z: -3.49 cb: 1.43 shift=0.3164 cc_mask=0.7398 cycle: 4 start: weight= 0.1540 bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.1540 bond: 0.011 angle: 1.91 clash: 6.5 rota: 4.35 rama: f: 95.95 o: 0.00 Z: -2.44 cb: 0.00 shift=0.2721 cc_mask=0.7302 cycle: 5 start: weight= 0.1078 bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.1078 bond: 0.010 angle: 1.82 clash: 2.5 rota: 4.35 rama: f: 97.30 o: 0.00 Z: -1.59 cb: 0.00 shift=0.2418 cc_mask=0.7218 cycle: 6 start: weight= 0.0539 bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.0539 bond: 0.009 angle: 1.77 clash: 0.8 rota: 4.35 rama: f: 98.65 o: 0.00 Z: -1.33 cb: 0.00 shift=0.2329 cc_mask=0.7094 cycle: 7 start: weight= 0.0377 bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.0377 bond: 0.009 angle: 1.77 clash: 0.8 rota: 4.35 rama: f: 98.65 o: 0.00 Z: -1.26 cb: 0.00 shift=0.2377 cc_mask=0.7056 cycle: 8 start: weight= 0.0264 bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.0264 bond: 0.009 angle: 1.76 clash: 0.8 rota: 4.35 rama: f: 98.65 o: 0.00 Z: -1.23 cb: 0.00 shift=0.2386 cc_mask=0.7026 cycle: 9 start: weight= 0.0132 bond: 0.003 angle: 0.86 clash: 9.8 rota: 1.45 rama: f: 95.95 o: 0.00 Z: -0.74 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.0132 bond: 0.009 angle: 1.76 clash: 0.8 rota: 4.35 rama: f: 98.65 o: 0.00 Z: -1.18 cb: 0.00 shift=0.2483 cc_mask=0.6987 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.013207683770774178 start: weight= 0.0132 bond: 0.009 angle: 1.76 clash: 0.8 rota: 4.35 rama: f: 98.65 o: 0.00 Z: -1.18 cb: 0.00 shift=0.0000 cc_mask=0.7101 final: weight= 0.0132 bond: 0.009 angle: 1.76 clash: 0.8 rota: 4.35 rama: f: 98.65 o: 0.00 Z: -1.15 cb: 0.00 shift=0.2485 cc_mask=0.6987 start: weight= 0.0132 bond: 0.009 angle: 1.76 clash: 0.8 rota: 4.35 rama: f: 98.65 o: 0.00 Z: -1.15 cb: 0.00 shift=0.2485 cc_mask=0.6987 final: weight= 0.0132 bond: 0.009 angle: 1.70 clash: 0.0 rota: 4.35 rama: f: 97.30 o: 0.00 Z: -0.25 cb: 0.00 shift=0.3524 cc_mask=0.6956 start: weight= 0.0132 bond: 0.009 angle: 1.70 clash: 0.0 rota: 4.35 rama: f: 97.30 o: 0.00 Z: -0.25 cb: 0.00 shift=0.3524 cc_mask=0.6956 final: weight= 0.0132 bond: 0.009 angle: 1.71 clash: 0.0 rota: 4.35 rama: f: 97.30 o: 0.00 Z: -0.38 cb: 0.00 shift=0.4091 cc_mask=0.6938 start: weight= 0.0132 bond: 0.009 angle: 1.71 clash: 0.0 rota: 4.35 rama: f: 97.30 o: 0.00 Z: -0.38 cb: 0.00 shift=0.4091 cc_mask=0.6938 final: weight= 0.0132 bond: 0.009 angle: 1.72 clash: 0.0 rota: 4.35 rama: f: 97.30 o: 0.00 Z: 0.02 cb: 0.00 shift=0.4576 cc_mask=0.6903 start: weight= 0.0132 bond: 0.009 angle: 1.72 clash: 0.0 rota: 4.35 rama: f: 97.30 o: 0.00 Z: 0.02 cb: 0.00 shift=0.4576 cc_mask=0.6903 final: weight= 0.0132 bond: 0.009 angle: 1.72 clash: 0.0 rota: 5.80 rama: f: 95.95 o: 0.00 Z: -0.09 cb: 0.00 shift=0.5065 cc_mask=0.6868 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.026 606 Z= 0.473 ANGLE : 1.719 9.441 814 Z= 0.884 CHIRALITY : 0.120 0.380 97 PLANARITY : 0.019 0.142 105 DIHEDRAL : 15.183 94.269 239 MIN NONBONDED DISTANCE : 2.656 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.00 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.05 % FAVORED : 95.95 % ROTAMER: OUTLIERS : 5.80 % ALLOWED : 4.35 % FAVORED : 89.86 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 1.37 % 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: -0.09 (1.04), RESIDUES: 74 HELIX: -2.05 (1.02), RESIDUES: 12 SHEET: -1.26 (1.01), RESIDUES: 25 LOOP : 1.94 (1.19), RESIDUES: 37 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.010 0.003 ARG K 274 TYR 0.062 0.028 TYR K 259 PHE 0.008 0.004 PHE K 245 HIS 0.002 0.002 HIS K 268 Resolution of map is: 3.8196 Map-model correlation coefficient (CC) CC_mask : 0.6868 =============================================================================== Job complete usr+sys time: 185.86 seconds wall clock time: 3 minutes 36.56 seconds (216.56 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)