Starting qr.refine on Sun May 19 16:06:01 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6y9w_10739.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6y9w_10739.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/6y9w_10739.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6y9w_10739.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6y9w_10739.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/6y9w_10739.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 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: (109.18, 114.48, 87.98, 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: 1.26 Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Time building geometry restraints manager: 1.45 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 - 1.48: 1345 1.48 - 1.65: 1526 1.65 - 1.82: 48 Bond restraints: 6942 Sorted by residual: bond pdb=" C ASN B 121 " pdb=" O ASN B 121 " ideal model delta sigma weight residual 1.231 1.247 -0.016 2.00e-02 2.50e+03 6.41e-01 bond pdb=" N PRO N 157 " pdb=" CA PRO N 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 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 5.68e-01 bond pdb=" C ILE B 6 " pdb=" N GLN B 7 " ideal model delta sigma weight residual 1.329 1.339 -0.010 1.40e-02 5.10e+03 5.61e-01 bond pdb=" N PRO B 157 " pdb=" CA PRO B 157 " ideal model delta sigma weight residual 1.466 1.477 -0.011 1.50e-02 4.44e+03 5.48e-01 ... (remaining 6937 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.03: 209 107.03 - 113.77: 8402 113.77 - 120.50: 2190 120.50 - 127.23: 1760 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 110.50 115.82 -5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" C ILE B 6 " pdb=" N GLN B 7 " pdb=" CA GLN B 7 " ideal model delta sigma weight residual 121.70 126.75 -5.05 1.80e+00 3.09e-01 7.88e+00 angle pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" N PRO A 122 " ideal model delta sigma weight residual 116.90 119.86 -2.96 1.50e+00 4.44e-01 3.91e+00 angle pdb=" CA ILE A 37 " pdb=" C ILE A 37 " pdb=" N PRO A 38 " ideal model delta sigma weight residual 116.90 119.82 -2.92 1.50e+00 4.44e-01 3.80e+00 angle pdb=" CA ASN B 121 " pdb=" C ASN B 121 " pdb=" N PRO B 122 " ideal model delta sigma weight residual 116.90 119.81 -2.91 1.50e+00 4.44e-01 3.78e+00 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 2920 14.62 - 29.25: 218 29.25 - 43.87: 95 43.87 - 58.49: 39 58.49 - 73.11: 6 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 -110.81 24.81 1 1.00e+01 1.00e-02 8.86e+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 -110.80 24.80 1 1.00e+01 1.00e-02 8.85e+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 -131.99 -48.01 3 1.50e+01 4.44e-03 8.58e+00 ... (remaining 3275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 348 0.028 - 0.056: 124 0.056 - 0.084: 36 0.084 - 0.112: 21 0.112 - 0.139: 5 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 4.86e-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 2.57 -0.13 2.00e-01 2.50e+01 4.48e-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 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO A 38 " -0.083 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 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 34 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " 0.017 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 2.79e-02 1.24e+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: 1.51 - 2.13: 506 2.13 - 2.74: 11248 2.74 - 3.36: 19045 3.36 - 3.98: 23772 3.98 - 4.60: 35522 Nonbonded interactions: 90093 Sorted by model distance: nonbonded pdb=" OE1 GLN B 179 " pdb="HD21 ASN B 183 " model vdw 1.507 1.800 nonbonded pdb=" OE1 GLN N 179 " pdb="HD21 ASN N 183 " model vdw 1.509 1.800 nonbonded pdb=" O ASN B 195 " pdb=" H LYS B 199 " model vdw 1.537 1.800 nonbonded pdb=" O ASN N 195 " pdb=" H LYS N 199 " model vdw 1.537 1.800 nonbonded pdb=" O SER A 44 " pdb=" HZ3 LYS A 131 " model vdw 1.593 1.800 ... (remaining 90088 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 : 0.918 5.933 4772 Z= 0.443 CHIRALITY : 0.037 0.139 534 PLANARITY : 0.004 0.048 625 DIHEDRAL : 11.751 73.114 1334 MIN NONBONDED DISTANCE : 2.336 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.60 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: -0.69 (0.38), RESIDUES: 434 HELIX: -0.08 (0.30), RESIDUES: 280 SHEET: -3.20 (0.75), RESIDUES: 9 LOOP : -0.77 (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 130 PHE 0.004 0.001 PHE A 32 TRP 0.006 0.001 TRP N 184 HIS 0.002 0.001 HIS A 84 Resolution of map is: 4.2006 Map-model correlation coefficient (CC) CC_mask : 0.7759 weight= None bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 Initial weight estimate from ratio of grad norms: 0.6071935168869084 cycle: 0 start: weight= 0.6072 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.6072 bond: 0.029 angle: 3.23 clash: 67.6 rota: 9.63 rama: f: 80.18 o: 3.69 Z: -6.49 cb: 3.64 shift=0.7995 cc_mask=0.8379 cycle: 1 start: weight= 0.4250 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.4250 bond: 0.023 angle: 2.67 clash: 38.7 rota: 4.81 rama: f: 89.17 o: 0.46 Z: -5.86 cb: 0.97 shift=0.6911 cc_mask=0.8314 cycle: 2 start: weight= 0.2975 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.2975 bond: 0.019 angle: 2.28 clash: 24.2 rota: 3.48 rama: f: 93.55 o: 0.00 Z: -5.28 cb: 0.00 shift=0.5917 cc_mask=0.8243 cycle: 3 start: weight= 0.1488 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.1488 bond: 0.014 angle: 1.79 clash: 4.2 rota: 1.07 rama: f: 98.62 o: 0.00 Z: -3.64 cb: 0.00 shift=0.4206 cc_mask=0.8109 cycle: 4 start: weight= 0.1041 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.1041 bond: 0.012 angle: 1.64 clash: 1.7 rota: 0.80 rama: f: 98.85 o: 0.00 Z: -2.93 cb: 0.00 shift=0.3556 cc_mask=0.8040 cycle: 5 start: weight= 0.0729 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.0729 bond: 0.011 angle: 1.57 clash: 1.2 rota: 0.27 rama: f: 98.85 o: 0.00 Z: -2.25 cb: 0.00 shift=0.2934 cc_mask=0.7978 cycle: 6 start: weight= 0.0364 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.0364 bond: 0.010 angle: 1.51 clash: 0.9 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -1.59 cb: 0.00 shift=0.2385 cc_mask=0.7886 cycle: 7 start: weight= 0.0255 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.0255 bond: 0.010 angle: 1.50 clash: 0.7 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -1.36 cb: 0.00 shift=0.2272 cc_mask=0.7856 cycle: 8 start: weight= 0.0179 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.0179 bond: 0.009 angle: 1.50 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -1.16 cb: 0.00 shift=0.2176 cc_mask=0.7833 cycle: 9 start: weight= 0.0089 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.0089 bond: 0.009 angle: 1.50 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -1.02 cb: 0.00 shift=0.2115 cc_mask=0.7800 cycle: 10 start: weight= 0.0063 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.0063 bond: 0.009 angle: 1.49 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -1.00 cb: 0.00 shift=0.2124 cc_mask=0.7790 cycle: 11 start: weight= 0.0044 bond: 0.004 angle: 0.92 clash: 1.6 rota: 0.80 rama: f: 97.70 o: 0.00 Z: -0.69 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.0044 bond: 0.009 angle: 1.50 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -1.01 cb: 0.00 shift=0.2104 cc_mask=0.7785 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0043754372416789575 start: weight= 0.0044 bond: 0.009 angle: 1.50 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -1.01 cb: 0.00 shift=0.0000 cc_mask=0.7759 final: weight= 0.0044 bond: 0.009 angle: 1.50 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -1.01 cb: 0.00 shift=0.2111 cc_mask=0.7784 start: weight= 0.0044 bond: 0.009 angle: 1.50 clash: 0.6 rota: 0.27 rama: f: 99.08 o: 0.00 Z: -1.01 cb: 0.00 shift=0.2111 cc_mask=0.7784 final: weight= 0.0044 bond: 0.009 angle: 1.45 clash: 0.7 rota: 0.27 rama: f: 99.31 o: 0.00 Z: -1.13 cb: 0.00 shift=0.2951 cc_mask=0.7736 start: weight= 0.0044 bond: 0.009 angle: 1.45 clash: 0.7 rota: 0.27 rama: f: 99.31 o: 0.00 Z: -1.13 cb: 0.00 shift=0.2951 cc_mask=0.7736 final: weight= 0.0044 bond: 0.009 angle: 1.47 clash: 0.9 rota: 0.27 rama: f: 99.31 o: 0.00 Z: -1.27 cb: 0.00 shift=0.3665 cc_mask=0.7695 start: weight= 0.0044 bond: 0.009 angle: 1.47 clash: 0.9 rota: 0.27 rama: f: 99.31 o: 0.00 Z: -1.27 cb: 0.00 shift=0.3665 cc_mask=0.7695 final: weight= 0.0044 bond: 0.009 angle: 1.45 clash: 0.9 rota: 0.27 rama: f: 99.54 o: 0.00 Z: -1.46 cb: 0.00 shift=0.4119 cc_mask=0.7664 start: weight= 0.0044 bond: 0.009 angle: 1.45 clash: 0.9 rota: 0.27 rama: f: 99.54 o: 0.00 Z: -1.46 cb: 0.00 shift=0.4119 cc_mask=0.7664 final: weight= 0.0044 bond: 0.009 angle: 1.47 clash: 0.6 rota: 0.27 rama: f: 98.85 o: 0.00 Z: -1.68 cb: 0.00 shift=0.4472 cc_mask=0.7641 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.050 3510 Z= 0.476 ANGLE : 1.470 9.572 4772 Z= 0.786 CHIRALITY : 0.113 0.358 534 PLANARITY : 0.012 0.112 625 DIHEDRAL : 13.318 121.263 1334 MIN NONBONDED DISTANCE : 2.628 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.58 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.15 % FAVORED : 98.85 % ROTAMER: OUTLIERS : 0.27 % ALLOWED : 4.01 % FAVORED : 95.72 % 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: -1.68 (0.34), RESIDUES: 434 HELIX: -1.30 (0.25), RESIDUES: 281 SHEET: -2.78 (0.90), RESIDUES: 18 LOOP : 0.09 (0.50), RESIDUES: 135 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.017 0.004 ARG A 97 TYR 0.064 0.012 TYR B 145 PHE 0.034 0.010 PHE A 32 TRP 0.077 0.019 TRP B 80 HIS 0.003 0.001 HIS A 12 Resolution of map is: 4.2006 Map-model correlation coefficient (CC) CC_mask : 0.7641 =============================================================================== Job complete usr+sys time: 694.03 seconds wall clock time: 12 minutes 29.10 seconds (749.10 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)