Starting qr.refine on Sun May 19 14:21:10 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qjx_18453.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qjx_18453.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/8qjx_18453.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qjx_18453.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qjx_18453.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8qjx_18453.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 318": "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: 3038 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3038 Classifications: {'peptide': 197} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Time building chain proxies: 0.43, per 1000 atoms: 0.14 Number of scatterers: 3038 At special positions: 0 Unit cell: (63.7, 58.5, 66.3, 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 310 8.00 N 258 7.00 C 971 6.00 H 1490 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: 0.55 Adding C-beta torsion restraints... Number of C-beta restraints generated: 376 Time building geometry restraints manager: 0.64 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: 1486 1.14 - 1.31: 262 1.31 - 1.47: 661 1.47 - 1.64: 648 1.64 - 1.81: 14 Bond restraints: 3071 Sorted by residual: bond pdb=" C TYR A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.341 1.329 0.012 1.60e-02 3.91e+03 5.34e-01 bond pdb=" C ASN A 130 " pdb=" N ILE A 131 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 4.98e-01 bond pdb=" C THR A 214 " pdb=" O THR A 214 " ideal model delta sigma weight residual 1.231 1.244 -0.013 2.00e-02 2.50e+03 4.19e-01 bond pdb=" CA THR A 165 " pdb=" CB THR A 165 " ideal model delta sigma weight residual 1.540 1.523 0.017 2.70e-02 1.37e+03 3.90e-01 bond pdb=" C PHE A 269 " pdb=" N PRO A 270 " ideal model delta sigma weight residual 1.341 1.332 0.009 1.60e-02 3.91e+03 3.02e-01 ... (remaining 3066 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 99 107.46 - 114.09: 3589 114.09 - 120.72: 1009 120.72 - 127.35: 793 127.35 - 133.98: 15 Bond angle restraints: 5505 Sorted by residual: angle pdb=" CA THR A 214 " pdb=" C THR A 214 " pdb=" N PRO A 215 " ideal model delta sigma weight residual 116.90 119.81 -2.91 1.50e+00 4.44e-01 3.77e+00 angle pdb=" N SER A 220 " pdb=" CA SER A 220 " pdb=" C SER A 220 " ideal model delta sigma weight residual 111.00 105.60 5.40 2.80e+00 1.28e-01 3.72e+00 angle pdb=" CA PHE A 269 " pdb=" C PHE A 269 " pdb=" N PRO A 270 " ideal model delta sigma weight residual 116.90 119.77 -2.87 1.50e+00 4.44e-01 3.67e+00 angle pdb=" C ALA A 171 " pdb=" N PHE A 172 " pdb=" CA PHE A 172 " ideal model delta sigma weight residual 121.70 125.05 -3.35 1.80e+00 3.09e-01 3.47e+00 angle pdb=" N PHE A 172 " pdb=" CA PHE A 172 " pdb=" C PHE A 172 " ideal model delta sigma weight residual 111.00 106.25 4.75 2.80e+00 1.28e-01 2.87e+00 ... (remaining 5500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 1383 15.22 - 30.44: 57 30.44 - 45.67: 19 45.67 - 60.89: 12 60.89 - 76.11: 4 Dihedral angle restraints: 1475 sinusoidal: 784 harmonic: 691 Sorted by residual: dihedral pdb=" CA LEU A 134 " pdb=" CB LEU A 134 " pdb=" CG LEU A 134 " pdb=" CD1 LEU A 134 " ideal model delta sinusoidal sigma weight residual 180.00 133.41 46.59 3 1.50e+01 4.44e-03 8.36e+00 dihedral pdb=" N ASN A 181 " pdb=" CA ASN A 181 " pdb=" CB ASN A 181 " pdb=" CG ASN A 181 " ideal model delta sinusoidal sigma weight residual -60.00 -102.72 42.72 3 1.50e+01 4.44e-03 7.67e+00 dihedral pdb=" CB MET A 236 " pdb=" CG MET A 236 " pdb=" SD MET A 236 " pdb=" CE MET A 236 " ideal model delta sinusoidal sigma weight residual 60.00 102.07 -42.07 3 1.50e+01 4.44e-03 7.54e+00 ... (remaining 1472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 138 0.027 - 0.054: 79 0.054 - 0.082: 15 0.082 - 0.109: 8 0.109 - 0.136: 11 Chirality restraints: 251 Sorted by residual: chirality pdb=" CA ILE A 290 " pdb=" N ILE A 290 " pdb=" C ILE A 290 " pdb=" CB ILE A 290 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 248 not shown) Planarity restraints: 467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 172 " 0.010 2.00e-02 2.50e+03 5.22e-03 8.18e-01 pdb=" CG PHE A 172 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 172 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 172 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 172 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 172 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 172 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 172 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 172 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 172 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 172 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 296 " 0.007 2.00e-02 2.50e+03 3.70e-03 5.47e-01 pdb=" CG TRP A 296 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP A 296 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 296 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 296 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 296 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 296 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 296 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 296 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 296 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 296 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP A 296 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 296 " -0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 296 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 296 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 296 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 139 " 0.010 5.00e-02 4.00e+02 1.48e-02 3.51e-01 pdb=" N PRO A 140 " -0.026 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " 0.008 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " 0.008 5.00e-02 4.00e+02 ... (remaining 464 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 217 2.14 - 2.76: 5314 2.76 - 3.37: 8197 3.37 - 3.99: 11463 3.99 - 4.60: 16553 Nonbonded interactions: 41744 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 219 " pdb=" O GLY A 221 " model vdw 1.528 1.800 nonbonded pdb=" OD1 ASN A 278 " pdb=" H CYS A 289 " model vdw 1.576 1.800 nonbonded pdb="HH12 ARG A 322 " pdb=" OD1 ASP A 325 " model vdw 1.579 1.800 nonbonded pdb=" H TYR A 260 " pdb=" OG SER A 314 " model vdw 1.590 1.800 nonbonded pdb=" O PHE A 235 " pdb=" HH TYR A 320 " model vdw 1.632 1.800 ... (remaining 41739 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 310 7.97 2 N 258 6.97 2 C 971 5.97 2 H 1490 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 0.017 1581 Z= 0.166 ANGLE : 0.963 5.400 2158 Z= 0.442 CHIRALITY : 0.042 0.136 251 PLANARITY : 0.002 0.015 278 DIHEDRAL : 10.696 76.109 559 MIN NONBONDED DISTANCE : 2.417 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.32 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 4.62 % FAVORED : 95.38 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 5.71 % FAVORED : 94.29 % 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: -0.77 (0.59), RESIDUES: 195 HELIX: -4.01 (0.67), RESIDUES: 6 SHEET: -0.37 (0.57), RESIDUES: 72 LOOP : -0.31 (0.60), RESIDUES: 117 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.001 0.000 ARG A 249 TYR 0.009 0.001 TYR A 174 PHE 0.014 0.001 PHE A 172 TRP 0.012 0.001 TRP A 296 HIS 0.002 0.001 HIS A 218 Resolution of map is: 3.4929 Map-model correlation coefficient (CC) CC_mask : 0.8745 weight= None bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 Initial weight estimate from ratio of grad norms: 0.5211665104624618 cycle: 0 start: weight= 0.5212 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.5212 bond: 0.028 angle: 2.25 clash: 8.6 rota: 0.00 rama: f: 96.41 o: 0.00 Z: -2.84 cb: 1.06 shift=0.2556 cc_mask=0.9012 cycle: 1 start: weight= 0.3648 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.3648 bond: 0.023 angle: 1.96 clash: 5.3 rota: 0.00 rama: f: 96.92 o: 0.00 Z: -2.01 cb: 0.53 shift=0.2404 cc_mask=0.8978 cycle: 2 start: weight= 0.2554 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.2554 bond: 0.018 angle: 1.78 clash: 3.0 rota: 0.00 rama: f: 96.92 o: 0.00 Z: -1.58 cb: 0.53 shift=0.2326 cc_mask=0.8944 cycle: 3 start: weight= 0.1277 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.1277 bond: 0.013 angle: 1.62 clash: 1.3 rota: 0.00 rama: f: 96.41 o: 0.00 Z: -1.27 cb: 0.53 shift=0.2143 cc_mask=0.8883 cycle: 4 start: weight= 0.0894 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.0894 bond: 0.012 angle: 1.59 clash: 1.0 rota: 0.00 rama: f: 96.92 o: 0.00 Z: -1.14 cb: 0.53 shift=0.2057 cc_mask=0.8858 cycle: 5 start: weight= 0.0626 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.0626 bond: 0.011 angle: 1.57 clash: 0.7 rota: 0.00 rama: f: 96.41 o: 0.00 Z: -1.03 cb: 0.53 shift=0.2010 cc_mask=0.8829 cycle: 6 start: weight= 0.0313 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.0313 bond: 0.010 angle: 1.55 clash: 0.3 rota: 0.00 rama: f: 96.92 o: 0.00 Z: -0.96 cb: 0.53 shift=0.1936 cc_mask=0.8791 cycle: 7 start: weight= 0.0219 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.0219 bond: 0.010 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.96 cb: 0.53 shift=0.1937 cc_mask=0.8779 cycle: 8 start: weight= 0.0153 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.0153 bond: 0.010 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.96 cb: 0.53 shift=0.1935 cc_mask=0.8771 cycle: 9 start: weight= 0.0077 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.0077 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.96 cb: 0.53 shift=0.1946 cc_mask=0.8759 cycle: 10 start: weight= 0.0054 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.0054 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.96 cb: 0.53 shift=0.1931 cc_mask=0.8754 cycle: 11 start: weight= 0.0038 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.0038 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.95 cb: 0.53 shift=0.1936 cc_mask=0.8751 cycle: 12 start: weight= 0.0019 bond: 0.003 angle: 0.96 clash: 1.3 rota: 0.00 rama: f: 95.38 o: 0.00 Z: -0.77 cb: 0.00 shift=0.0000 cc_mask=0.8745 final: weight= 0.0019 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 96.92 o: 0.00 Z: -0.95 cb: 0.53 shift=0.1954 cc_mask=0.8749 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0018777632629253188 start: weight= 0.0019 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 96.92 o: 0.00 Z: -0.95 cb: 0.53 shift=0.0000 cc_mask=0.8745 final: weight= 0.0019 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.95 cb: 0.53 shift=0.1924 cc_mask=0.8748 start: weight= 0.0019 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.95 cb: 0.53 shift=0.1924 cc_mask=0.8748 final: weight= 0.0019 bond: 0.009 angle: 1.55 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.89 cb: 0.53 shift=0.2784 cc_mask=0.8718 start: weight= 0.0019 bond: 0.009 angle: 1.55 clash: 0.3 rota: 0.00 rama: f: 97.44 o: 0.00 Z: -0.89 cb: 0.53 shift=0.2784 cc_mask=0.8718 final: weight= 0.0019 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.57 rama: f: 96.92 o: 0.00 Z: -0.77 cb: 0.53 shift=0.3242 cc_mask=0.8700 start: weight= 0.0019 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.57 rama: f: 96.92 o: 0.00 Z: -0.77 cb: 0.53 shift=0.3242 cc_mask=0.8700 final: weight= 0.0019 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 96.92 o: 0.00 Z: -1.00 cb: 0.53 shift=0.3591 cc_mask=0.8677 start: weight= 0.0019 bond: 0.009 angle: 1.56 clash: 0.3 rota: 0.00 rama: f: 96.92 o: 0.00 Z: -1.00 cb: 0.53 shift=0.3591 cc_mask=0.8677 final: weight= 0.0019 bond: 0.009 angle: 1.57 clash: 0.3 rota: 0.00 rama: f: 96.92 o: 0.00 Z: -1.05 cb: 0.53 shift=0.3969 cc_mask=0.8641 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.030 1581 Z= 0.485 ANGLE : 1.570 9.415 2158 Z= 0.822 CHIRALITY : 0.113 0.485 251 PLANARITY : 0.010 0.073 278 DIHEDRAL : 10.840 99.305 559 MIN NONBONDED DISTANCE : 2.565 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.33 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 3.08 % FAVORED : 96.92 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 3.43 % FAVORED : 96.57 % CBETA DEVIATIONS : 0.53 % 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: -1.05 (0.57), RESIDUES: 195 HELIX: -3.26 (1.10), RESIDUES: 12 SHEET: -1.22 (0.56), RESIDUES: 66 LOOP : 0.07 (0.57), RESIDUES: 117 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.021 0.005 ARG A 249 TYR 0.069 0.015 TYR A 242 PHE 0.051 0.012 PHE A 172 TRP 0.140 0.029 TRP A 296 HIS 0.002 0.001 HIS A 188 Resolution of map is: 3.4929 Map-model correlation coefficient (CC) CC_mask : 0.8641 =============================================================================== Job complete usr+sys time: 353.28 seconds wall clock time: 6 minutes 39.75 seconds (399.75 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)