Starting qr.refine on Sun May 19 15:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8esa_28573.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8esa_28573.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/8esa_28573.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8esa_28573.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8esa_28573.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8esa_28573.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 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 63": "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: 6101 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 4308 Inner-chain residues flagged as termini: ['pdbres="GLN A 224 "', 'pdbres="THR A 228 "'] Classifications: {'peptide': 273} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1624 Classifications: {'peptide': 99} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 169 Classifications: {'peptide': 12} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 11} Time building chain proxies: 0.73, per 1000 atoms: 0.12 Number of scatterers: 6101 At special positions: 0 Unit cell: (85, 66.3, 68, 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 14 16.00 O 597 8.00 N 563 7.00 C 1970 6.00 H 2957 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS C 12 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.04 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: 1.05 Adding C-beta torsion restraints... Number of C-beta restraints generated: 716 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2957 1.15 - 1.31: 526 1.31 - 1.48: 1402 1.48 - 1.65: 1284 1.65 - 1.82: 20 Bond restraints: 6189 Sorted by residual: bond pdb=" C GLY A 18 " pdb=" N GLU A 19 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 1.05e+00 bond pdb=" C CYS A 164 " pdb=" N VAL A 165 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.63e-01 bond pdb=" C ASP A 102 " pdb=" N VAL A 103 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.59e-01 bond pdb=" C GLU A 46 " pdb=" N PRO A 47 " ideal model delta sigma weight residual 1.341 1.330 0.011 1.60e-02 3.91e+03 4.89e-01 bond pdb=" C ALA A 49 " pdb=" O ALA A 49 " ideal model delta sigma weight residual 1.231 1.245 -0.014 2.00e-02 2.50e+03 4.71e-01 ... (remaining 6184 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.01: 127 107.01 - 113.77: 6998 113.77 - 120.52: 2039 120.52 - 127.27: 1871 127.27 - 134.02: 58 Bond angle restraints: 11093 Sorted by residual: angle pdb=" CA ARG B 97 " pdb=" C ARG B 97 " pdb=" N ASP B 98 " ideal model delta sigma weight residual 116.20 120.75 -4.55 2.00e+00 2.50e-01 5.18e+00 angle pdb=" C CYS A 164 " pdb=" N VAL A 165 " pdb=" CA VAL A 165 " ideal model delta sigma weight residual 121.70 117.94 3.76 1.80e+00 3.09e-01 4.37e+00 angle pdb=" CA ARG B 97 " pdb=" C ARG B 97 " pdb=" O ARG B 97 " ideal model delta sigma weight residual 120.80 117.57 3.23 1.70e+00 3.46e-01 3.62e+00 angle pdb=" CA THR B 71 " pdb=" C THR B 71 " pdb=" N PRO B 72 " ideal model delta sigma weight residual 116.90 119.70 -2.80 1.50e+00 4.44e-01 3.49e+00 angle pdb=" N TYR A 209 " pdb=" CA TYR A 209 " pdb=" C TYR A 209 " ideal model delta sigma weight residual 111.00 105.82 5.18 2.80e+00 1.28e-01 3.42e+00 ... (remaining 11088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 2664 16.43 - 32.86: 189 32.86 - 49.29: 60 49.29 - 65.72: 26 65.72 - 82.15: 3 Dihedral angle restraints: 2942 sinusoidal: 1552 harmonic: 1390 Sorted by residual: dihedral pdb=" CA TYR A 27 " pdb=" C TYR A 27 " pdb=" N VAL A 28 " pdb=" CA VAL A 28 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 dihedral pdb=" CA ARG B 81 " pdb=" CB ARG B 81 " pdb=" CG ARG B 81 " pdb=" CD ARG B 81 " ideal model delta sinusoidal sigma weight residual -60.00 -107.41 47.41 3 1.50e+01 4.44e-03 8.49e+00 dihedral pdb=" CA ARG A 256 " pdb=" CB ARG A 256 " pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " ideal model delta sinusoidal sigma weight residual -180.00 -134.14 -45.86 3 1.50e+01 4.44e-03 8.24e+00 ... (remaining 2939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 275 0.029 - 0.059: 119 0.059 - 0.088: 25 0.088 - 0.117: 18 0.117 - 0.146: 7 Chirality restraints: 444 Sorted by residual: chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE A 23 " pdb=" N ILE A 23 " pdb=" C ILE A 23 " pdb=" CB ILE A 23 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 441 not shown) Planarity restraints: 938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 49 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 50 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C LEU A 160 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 160 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU A 161 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 249 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 250 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 250 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 250 " 0.015 5.00e-02 4.00e+02 ... (remaining 935 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 503 2.18 - 2.78: 10875 2.78 - 3.39: 15584 3.39 - 3.99: 21491 3.99 - 4.60: 31973 Nonbonded interactions: 80426 Sorted by model distance: nonbonded pdb=" OD1 ASN B 21 " pdb=" H PHE B 22 " model vdw 1.575 1.800 nonbonded pdb=" OE1 GLU A 58 " pdb=" H GLU A 58 " model vdw 1.578 1.800 nonbonded pdb=" HE ARG A 21 " pdb=" OD2 ASP A 39 " model vdw 1.628 1.800 nonbonded pdb=" H LYS B 41 " pdb=" O GLU B 44 " model vdw 1.656 1.800 nonbonded pdb=" OD1 ASP A 77 " pdb=" H VAL C 10 " model vdw 1.684 1.800 ... (remaining 80421 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 14 15.96 2 O 597 7.97 2 N 563 6.97 2 C 1970 5.97 2 H 2957 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 0.028 3232 Z= 0.185 ANGLE : 0.900 6.702 4383 Z= 0.418 CHIRALITY : 0.040 0.146 444 PLANARITY : 0.003 0.040 575 DIHEDRAL : 12.874 82.146 1180 MIN NONBONDED DISTANCE : 2.267 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.80 RAMACHANDRAN PLOT: OUTLIERS : 0.53 % ALLOWED : 6.38 % FAVORED : 93.09 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.60 % FAVORED : 99.40 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 11.76 % 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: -1.41 (0.41), RESIDUES: 376 HELIX: 0.82 (0.59), RESIDUES: 66 SHEET: -0.63 (0.45), RESIDUES: 129 LOOP : -1.85 (0.41), RESIDUES: 181 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.000 ARG A 21 TYR 0.011 0.001 TYR A 159 PHE 0.005 0.001 PHE A 208 TRP 0.007 0.001 TRP A 204 HIS 0.002 0.001 HIS A 70 Resolution of map is: 3.6352 Map-model correlation coefficient (CC) CC_mask : 0.8344 weight= None bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 Initial weight estimate from ratio of grad norms: 0.28064515352298586 cycle: 0 start: weight= 0.2806 bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.2806 bond: 0.021 angle: 2.48 clash: 9.0 rota: 0.90 rama: f: 86.17 o: 1.33 Z: -4.86 cb: 1.68 shift=0.3139 cc_mask=0.8687 cycle: 1 start: weight= 0.1965 bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.1965 bond: 0.017 angle: 2.13 clash: 4.6 rota: 0.30 rama: f: 90.96 o: 0.27 Z: -4.11 cb: 0.56 shift=0.2801 cc_mask=0.8634 cycle: 2 start: weight= 0.1375 bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.1375 bond: 0.014 angle: 1.90 clash: 2.3 rota: 0.00 rama: f: 93.62 o: 0.27 Z: -3.29 cb: 0.00 shift=0.2561 cc_mask=0.8580 cycle: 3 start: weight= 0.0688 bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.0688 bond: 0.011 angle: 1.68 clash: 0.2 rota: 0.00 rama: f: 96.54 o: 0.00 Z: -2.01 cb: 0.00 shift=0.2338 cc_mask=0.8481 cycle: 4 start: weight= 0.0481 bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.0481 bond: 0.010 angle: 1.63 clash: 0.2 rota: 0.00 rama: f: 97.34 o: 0.00 Z: -1.67 cb: 0.00 shift=0.2326 cc_mask=0.8430 cycle: 5 start: weight= 0.0337 bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.0337 bond: 0.010 angle: 1.61 clash: 0.2 rota: 0.00 rama: f: 97.07 o: 0.00 Z: -1.34 cb: 0.00 shift=0.2320 cc_mask=0.8385 cycle: 6 start: weight= 0.0168 bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.0168 bond: 0.009 angle: 1.60 clash: 0.0 rota: 0.00 rama: f: 97.61 o: 0.00 Z: -1.06 cb: 0.00 shift=0.2391 cc_mask=0.8313 cycle: 7 start: weight= 0.0118 bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.0118 bond: 0.009 angle: 1.60 clash: 0.0 rota: 0.00 rama: f: 97.87 o: 0.00 Z: -0.97 cb: 0.00 shift=0.2386 cc_mask=0.8288 cycle: 8 start: weight= 0.0083 bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.0083 bond: 0.009 angle: 1.60 clash: 0.0 rota: 0.00 rama: f: 97.87 o: 0.00 Z: -0.91 cb: 0.00 shift=0.2407 cc_mask=0.8270 cycle: 9 start: weight= 0.0041 bond: 0.004 angle: 0.90 clash: 1.8 rota: 0.00 rama: f: 93.09 o: 0.53 Z: -1.41 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.0041 bond: 0.009 angle: 1.60 clash: 0.0 rota: 0.00 rama: f: 97.61 o: 0.00 Z: -0.87 cb: 0.00 shift=0.2457 cc_mask=0.8244 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.00412720270835322 start: weight= 0.0041 bond: 0.009 angle: 1.60 clash: 0.0 rota: 0.00 rama: f: 97.61 o: 0.00 Z: -0.87 cb: 0.00 shift=0.0000 cc_mask=0.8344 final: weight= 0.0041 bond: 0.009 angle: 1.60 clash: 0.0 rota: 0.00 rama: f: 97.61 o: 0.00 Z: -0.87 cb: 0.00 shift=0.2461 cc_mask=0.8244 start: weight= 0.0041 bond: 0.009 angle: 1.60 clash: 0.0 rota: 0.00 rama: f: 97.61 o: 0.00 Z: -0.87 cb: 0.00 shift=0.2461 cc_mask=0.8244 final: weight= 0.0041 bond: 0.009 angle: 1.57 clash: 0.3 rota: 0.00 rama: f: 97.87 o: 0.00 Z: -0.39 cb: 0.00 shift=0.3271 cc_mask=0.8186 start: weight= 0.0041 bond: 0.009 angle: 1.57 clash: 0.3 rota: 0.00 rama: f: 97.87 o: 0.00 Z: -0.39 cb: 0.00 shift=0.3271 cc_mask=0.8186 final: weight= 0.0041 bond: 0.009 angle: 1.60 clash: 0.0 rota: 0.00 rama: f: 97.61 o: 0.00 Z: -0.37 cb: 0.00 shift=0.3961 cc_mask=0.8120 start: weight= 0.0041 bond: 0.009 angle: 1.60 clash: 0.0 rota: 0.00 rama: f: 97.61 o: 0.00 Z: -0.37 cb: 0.00 shift=0.3961 cc_mask=0.8120 final: weight= 0.0041 bond: 0.009 angle: 1.59 clash: 0.2 rota: 0.30 rama: f: 97.61 o: 0.00 Z: -0.26 cb: 0.00 shift=0.4489 cc_mask=0.8062 start: weight= 0.0041 bond: 0.009 angle: 1.59 clash: 0.2 rota: 0.30 rama: f: 97.61 o: 0.00 Z: -0.26 cb: 0.00 shift=0.4489 cc_mask=0.8062 final: weight= 0.0041 bond: 0.009 angle: 1.60 clash: 0.2 rota: 0.30 rama: f: 97.61 o: 0.00 Z: -0.49 cb: 0.00 shift=0.4858 cc_mask=0.8019 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.030 3232 Z= 0.506 ANGLE : 1.604 9.725 4383 Z= 0.863 CHIRALITY : 0.103 0.305 444 PLANARITY : 0.019 0.168 575 DIHEDRAL : 12.605 81.761 1180 MIN NONBONDED DISTANCE : 2.579 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.16 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.39 % FAVORED : 97.61 % ROTAMER: OUTLIERS : 0.30 % ALLOWED : 1.20 % FAVORED : 98.49 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 11.76 % 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: -0.49 (0.39), RESIDUES: 376 HELIX: -0.30 (0.50), RESIDUES: 75 SHEET: -0.23 (0.42), RESIDUES: 137 LOOP : -0.21 (0.45), RESIDUES: 164 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.019 0.004 ARG A 82 TYR 0.050 0.014 TYR B 10 PHE 0.029 0.009 PHE A 9 TRP 0.116 0.024 TRP A 244 HIS 0.004 0.001 HIS A 191 Resolution of map is: 3.6352 Map-model correlation coefficient (CC) CC_mask : 0.8019 =============================================================================== Job complete usr+sys time: 537.97 seconds wall clock time: 9 minutes 48.43 seconds (588.43 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)