Starting qr.refine on Sun May 19 16:18:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6y9x_10740.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6y9x_10740.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/6y9x_10740.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6y9x_10740.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6y9x_10740.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6y9x_10740.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: 6867 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2265 Classifications: {'peptide': 146} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 134} Chain: "B" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3432 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "N" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1170 Classifications: {'peptide': 74} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 0.81, per 1000 atoms: 0.12 Number of scatterers: 6867 At special positions: 0 Unit cell: (95.4, 125.08, 85.86, 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 26 16.00 O 649 8.00 N 598 7.00 C 2162 6.00 H 3432 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS N 198 " - pdb=" SG CYS N 218 " 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: 1.27 Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Time building geometry restraints manager: 1.46 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: 3432 1.15 - 1.32: 591 1.32 - 1.49: 1346 1.49 - 1.65: 1525 1.65 - 1.82: 48 Bond restraints: 6942 Sorted by residual: bond pdb=" C HIS A 84 " pdb=" O HIS A 84 " ideal model delta sigma weight residual 1.231 1.249 -0.018 2.00e-02 2.50e+03 8.50e-01 bond pdb=" N PRO B 157 " pdb=" CA PRO B 157 " ideal model delta sigma weight residual 1.466 1.478 -0.012 1.50e-02 4.44e+03 6.08e-01 bond pdb=" C ASN B 121 " pdb=" O ASN B 121 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.98e-01 bond pdb=" C ASN A 121 " pdb=" O ASN A 121 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.76e-01 bond pdb=" N PRO N 157 " pdb=" CA PRO N 157 " ideal model delta sigma weight residual 1.466 1.476 -0.010 1.50e-02 4.44e+03 4.87e-01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 202 107.01 - 113.75: 8403 113.75 - 120.49: 2188 120.49 - 127.23: 1768 127.23 - 133.96: 58 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C ALA B 31 " pdb=" CA ALA B 31 " pdb=" CB ALA B 31 " ideal model delta sigma weight residual 110.50 115.71 -5.21 1.50e+00 4.44e-01 1.21e+01 angle pdb=" C ILE B 6 " pdb=" N GLN B 7 " pdb=" CA GLN B 7 " ideal model delta sigma weight residual 121.70 126.70 -5.00 1.80e+00 3.09e-01 7.73e+00 angle pdb=" CA ILE A 37 " pdb=" C ILE A 37 " pdb=" N PRO A 38 " ideal model delta sigma weight residual 116.90 119.88 -2.98 1.50e+00 4.44e-01 3.95e+00 angle pdb=" CA ASN B 121 " pdb=" C ASN B 121 " pdb=" N PRO B 122 " ideal model delta sigma weight residual 116.90 119.84 -2.94 1.50e+00 4.44e-01 3.85e+00 angle pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" N PRO A 122 " ideal model delta sigma weight residual 116.90 119.79 -2.89 1.50e+00 4.44e-01 3.72e+00 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 2918 14.70 - 29.40: 216 29.40 - 44.10: 100 44.10 - 58.81: 42 58.81 - 73.51: 2 Dihedral angle restraints: 3278 sinusoidal: 1853 harmonic: 1425 Sorted by residual: dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -111.00 25.00 1 1.00e+01 1.00e-02 8.99e+00 dihedral pdb=" CB CYS N 198 " pdb=" SG CYS N 198 " pdb=" SG CYS N 218 " pdb=" CB CYS N 218 " ideal model delta sinusoidal sigma weight residual -86.00 -110.92 24.92 1 1.00e+01 1.00e-02 8.94e+00 dihedral pdb=" CB MET N 215 " pdb=" CG MET N 215 " pdb=" SD MET N 215 " pdb=" CE MET N 215 " ideal model delta sinusoidal sigma weight residual -180.00 -131.88 -48.12 3 1.50e+01 4.44e-03 8.59e+00 ... (remaining 3275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 348 0.027 - 0.055: 121 0.055 - 0.082: 33 0.082 - 0.110: 26 0.110 - 0.137: 6 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 2 " pdb=" N ILE A 2 " pdb=" C ILE A 2 " pdb=" CB ILE A 2 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 531 not shown) Planarity restraints: 1031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 37 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 38 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 33 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 34 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 37 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 38 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " 0.015 5.00e-02 4.00e+02 ... (remaining 1028 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 502 2.12 - 2.74: 11160 2.74 - 3.36: 19049 3.36 - 3.98: 23799 3.98 - 4.60: 35425 Nonbonded interactions: 89935 Sorted by model distance: nonbonded pdb=" OE1 GLN N 179 " pdb="HD21 ASN N 183 " model vdw 1.503 1.800 nonbonded pdb=" OE1 GLN B 179 " pdb="HD21 ASN B 183 " model vdw 1.509 1.800 nonbonded pdb=" O ASN B 195 " pdb=" H LYS B 199 " model vdw 1.536 1.800 nonbonded pdb=" O ASN N 195 " pdb=" H LYS N 199 " model vdw 1.536 1.800 nonbonded pdb=" O SER A 44 " pdb=" HZ3 LYS A 131 " model vdw 1.593 1.800 ... (remaining 89930 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 26 15.96 2 O 649 7.97 2 N 598 6.97 2 C 2162 5.97 2 H 3432 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 0.024 3510 Z= 0.195 ANGLE : 0.914 5.925 4772 Z= 0.441 CHIRALITY : 0.037 0.137 534 PLANARITY : 0.004 0.047 625 DIHEDRAL : 11.743 73.507 1334 MIN NONBONDED DISTANCE : 2.370 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.46 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.30 % FAVORED : 97.70 % ROTAMER: OUTLIERS : 0.80 % ALLOWED : 2.67 % FAVORED : 96.52 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 6.45 % CIS-GENERAL : 0.25 % 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: -0.68 (0.38), RESIDUES: 434 HELIX: -0.08 (0.30), RESIDUES: 280 SHEET: -3.36 (0.65), RESIDUES: 9 LOOP : -0.74 (0.48), RESIDUES: 145 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.003 0.000 ARG A 18 TYR 0.006 0.001 TYR B 145 PHE 0.004 0.001 PHE A 32 TRP 0.005 0.001 TRP B 117 HIS 0.002 0.000 HIS B 12 Resolution of map is: 4.5654 Map-model correlation coefficient (CC) CC_mask : 0.7528 weight= None bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 Initial weight estimate from ratio of grad norms: 0.6844706997041967 cycle: 0 start: weight= 0.6845 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.6845 bond: 0.029 angle: 3.38 clash: 92.6 rota: 12.03 rama: f: 74.19 o: 5.07 Z: -6.91 cb: 5.10 shift=0.9210 cc_mask=0.8377 cycle: 1 start: weight= 0.4791 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.4791 bond: 0.023 angle: 2.82 clash: 52.6 rota: 5.88 rama: f: 83.18 o: 2.30 Z: -6.06 cb: 2.91 shift=0.7835 cc_mask=0.8288 cycle: 2 start: weight= 0.3354 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.3354 bond: 0.019 angle: 2.38 clash: 29.3 rota: 4.81 rama: f: 89.86 o: 0.46 Z: -5.45 cb: 1.70 shift=0.6544 cc_mask=0.8185 cycle: 3 start: weight= 0.1677 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.1677 bond: 0.014 angle: 1.88 clash: 6.0 rota: 1.34 rama: f: 97.00 o: 0.00 Z: -3.56 cb: 0.00 shift=0.4670 cc_mask=0.8008 cycle: 4 start: weight= 0.1174 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.1174 bond: 0.012 angle: 1.71 clash: 2.2 rota: 1.34 rama: f: 98.85 o: 0.00 Z: -2.73 cb: 0.00 shift=0.3748 cc_mask=0.7907 cycle: 5 start: weight= 0.0822 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.0822 bond: 0.011 angle: 1.61 clash: 1.3 rota: 1.07 rama: f: 98.85 o: 0.00 Z: -2.06 cb: 0.00 shift=0.3105 cc_mask=0.7811 cycle: 6 start: weight= 0.0411 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.0411 bond: 0.010 angle: 1.52 clash: 0.6 rota: 0.27 rama: f: 98.85 o: 0.00 Z: -1.35 cb: 0.00 shift=0.2419 cc_mask=0.7689 cycle: 7 start: weight= 0.0288 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.0288 bond: 0.010 angle: 1.51 clash: 0.6 rota: 0.27 rama: f: 98.85 o: 0.00 Z: -1.12 cb: 0.00 shift=0.2256 cc_mask=0.7642 cycle: 8 start: weight= 0.0201 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.0201 bond: 0.009 angle: 1.50 clash: 0.4 rota: 0.27 rama: f: 98.85 o: 0.00 Z: -1.06 cb: 0.00 shift=0.2141 cc_mask=0.7611 cycle: 9 start: weight= 0.0101 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.0101 bond: 0.009 angle: 1.50 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -0.98 cb: 0.00 shift=0.2106 cc_mask=0.7573 cycle: 10 start: weight= 0.0070 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.0070 bond: 0.009 angle: 1.50 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -0.99 cb: 0.00 shift=0.2107 cc_mask=0.7562 cycle: 11 start: weight= 0.0049 bond: 0.004 angle: 0.91 clash: 1.5 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.68 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.0049 bond: 0.009 angle: 1.49 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -0.99 cb: 0.00 shift=0.2111 cc_mask=0.7553 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.004932296717656816 start: weight= 0.0049 bond: 0.009 angle: 1.49 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -0.99 cb: 0.00 shift=0.0000 cc_mask=0.7528 final: weight= 0.0049 bond: 0.009 angle: 1.49 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -0.99 cb: 0.00 shift=0.2103 cc_mask=0.7553 start: weight= 0.0049 bond: 0.009 angle: 1.49 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -0.99 cb: 0.00 shift=0.2103 cc_mask=0.7553 final: weight= 0.0049 bond: 0.009 angle: 1.46 clash: 0.9 rota: 0.27 rama: f: 99.31 o: 0.00 Z: -1.10 cb: 0.00 shift=0.2967 cc_mask=0.7523 start: weight= 0.0049 bond: 0.009 angle: 1.46 clash: 0.9 rota: 0.27 rama: f: 99.31 o: 0.00 Z: -1.10 cb: 0.00 shift=0.2967 cc_mask=0.7523 final: weight= 0.0049 bond: 0.009 angle: 1.47 clash: 0.9 rota: 0.27 rama: f: 99.31 o: 0.00 Z: -1.17 cb: 0.00 shift=0.3677 cc_mask=0.7487 start: weight= 0.0049 bond: 0.009 angle: 1.47 clash: 0.9 rota: 0.27 rama: f: 99.31 o: 0.00 Z: -1.17 cb: 0.00 shift=0.3677 cc_mask=0.7487 final: weight= 0.0049 bond: 0.009 angle: 1.45 clash: 0.4 rota: 0.27 rama: f: 98.85 o: 0.00 Z: -1.32 cb: 0.00 shift=0.4098 cc_mask=0.7460 start: weight= 0.0049 bond: 0.009 angle: 1.45 clash: 0.4 rota: 0.27 rama: f: 98.85 o: 0.00 Z: -1.32 cb: 0.00 shift=0.4098 cc_mask=0.7460 final: weight= 0.0049 bond: 0.009 angle: 1.47 clash: 0.4 rota: 0.53 rama: f: 99.08 o: 0.00 Z: -1.61 cb: 0.00 shift=0.4475 cc_mask=0.7436 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.052 3510 Z= 0.476 ANGLE : 1.469 9.585 4772 Z= 0.786 CHIRALITY : 0.113 0.357 534 PLANARITY : 0.012 0.127 625 DIHEDRAL : 12.840 97.792 1334 MIN NONBONDED DISTANCE : 2.621 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.44 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 0.92 % FAVORED : 99.08 % ROTAMER: OUTLIERS : 0.53 % ALLOWED : 3.48 % FAVORED : 95.99 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 6.45 % CIS-GENERAL : 0.25 % 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: -1.61 (0.34), RESIDUES: 434 HELIX: -1.27 (0.24), RESIDUES: 274 SHEET: -2.75 (0.92), RESIDUES: 18 LOOP : 0.10 (0.48), RESIDUES: 142 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.019 0.004 ARG B 167 TYR 0.061 0.012 TYR B 145 PHE 0.036 0.010 PHE A 32 TRP 0.066 0.019 TRP B 184 HIS 0.004 0.001 HIS B 84 Resolution of map is: 4.5654 Map-model correlation coefficient (CC) CC_mask : 0.7436 =============================================================================== Job complete usr+sys time: 683.69 seconds wall clock time: 12 minutes 19.32 seconds (739.32 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)