Starting qr.refine on Sun May 19 17:05:57 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8e6k_27921.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8e6k_27921.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/8e6k_27921.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8e6k_27921.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8e6k_27921.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8e6k_27921.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 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 98": "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: 9223 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 5754 Classifications: {'peptide': 385} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "I" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1641 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1828 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 114} Time building chain proxies: 1.12, per 1000 atoms: 0.12 Number of scatterers: 9223 At special positions: 0 Unit cell: (110.2, 121.075, 84.1, 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 30 16.00 O 924 8.00 N 799 7.00 C 2969 6.00 H 4501 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 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: 1.67 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1106 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 4500 1.14 - 1.31: 773 1.31 - 1.48: 2087 1.48 - 1.65: 1949 1.65 - 1.82: 39 Bond restraints: 9348 Sorted by residual: bond pdb=" C GLN E 39 " pdb=" O GLN E 39 " ideal model delta sigma weight residual 1.231 1.253 -0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" C ARG E 38 " pdb=" N GLN E 39 " ideal model delta sigma weight residual 1.329 1.315 0.014 1.40e-02 5.10e+03 1.01e+00 bond pdb=" C GLN E 39 " pdb=" N PRO E 40 " ideal model delta sigma weight residual 1.341 1.326 0.015 1.60e-02 3.91e+03 9.28e-01 bond pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta sigma weight residual 1.466 1.479 -0.013 1.50e-02 4.44e+03 7.84e-01 bond pdb=" C ARG A 327 " pdb=" N PRO A 328 " ideal model delta sigma weight residual 1.341 1.328 0.013 1.60e-02 3.91e+03 7.06e-01 ... (remaining 9343 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 204 106.97 - 113.73: 10859 113.73 - 120.49: 2840 120.49 - 127.24: 2816 127.24 - 134.00: 79 Bond angle restraints: 16798 Sorted by residual: angle pdb=" C PRO E 14 " pdb=" N SER E 15 " pdb=" CA SER E 15 " ideal model delta sigma weight residual 121.70 126.99 -5.29 1.80e+00 3.09e-01 8.63e+00 angle pdb=" C SER I 30 " pdb=" CA SER I 30 " pdb=" CB SER I 30 " ideal model delta sigma weight residual 110.10 115.61 -5.51 1.90e+00 2.77e-01 8.41e+00 angle pdb=" C ASP A 357 " pdb=" CA ASP A 357 " pdb=" CB ASP A 357 " ideal model delta sigma weight residual 110.10 115.48 -5.38 1.90e+00 2.77e-01 8.03e+00 angle pdb=" C TRP E 35A" pdb=" N GLY E 35B" pdb=" CA GLY E 35B" ideal model delta sigma weight residual 121.70 116.81 4.89 1.80e+00 3.09e-01 7.38e+00 angle pdb=" C ASN A 309 " pdb=" N LEU A 310 " pdb=" CA LEU A 310 " ideal model delta sigma weight residual 121.70 126.55 -4.85 1.80e+00 3.09e-01 7.27e+00 ... (remaining 16793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 4088 15.41 - 30.83: 257 30.83 - 46.24: 109 46.24 - 61.65: 46 61.65 - 77.07: 7 Dihedral angle restraints: 4507 sinusoidal: 2406 harmonic: 2101 Sorted by residual: dihedral pdb=" CA TYR E 34 " pdb=" C TYR E 34 " pdb=" N TYR E 35 " pdb=" CA TYR E 35 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA VAL A 116 " pdb=" C VAL A 116 " pdb=" N ILE A 117 " pdb=" CA ILE A 117 " ideal model delta harmonic sigma weight residual 180.00 -162.48 -17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual 93.00 64.37 28.63 1 1.00e+01 1.00e-02 1.17e+01 ... (remaining 4504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 383 0.029 - 0.058: 222 0.058 - 0.087: 40 0.087 - 0.117: 46 0.117 - 0.146: 18 Chirality restraints: 709 Sorted by residual: chirality pdb=" CA ILE A 192 " pdb=" N ILE A 192 " pdb=" C ILE A 192 " pdb=" CB ILE A 192 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE E 37 " pdb=" N ILE E 37 " pdb=" C ILE E 37 " pdb=" CB ILE E 37 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A 349 " pdb=" N ILE A 349 " pdb=" C ILE A 349 " pdb=" CB ILE A 349 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 706 not shown) Planarity restraints: 1430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 161 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 162 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 66 " 0.093 9.50e-02 1.11e+02 3.12e-02 1.31e+00 pdb=" NE ARG E 66 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG E 66 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG E 66 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 66 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG E 66 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG E 66 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG E 66 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 66 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 412A" -0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 412B" 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 412B" -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 412B" -0.015 5.00e-02 4.00e+02 ... (remaining 1427 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.12: 622 2.12 - 2.74: 15115 2.74 - 3.36: 25938 3.36 - 3.98: 37090 3.98 - 4.60: 54207 Nonbonded interactions: 132972 Sorted by model distance: nonbonded pdb=" HG1 THR A 242 " pdb=" O TYR A 275 " model vdw 1.495 1.800 nonbonded pdb=" H TYR A 100 " pdb=" O SER A 445 " model vdw 1.497 1.800 nonbonded pdb=" H ARG E 38 " pdb=" O GLU E 46 " model vdw 1.537 1.800 nonbonded pdb=" O LYS A 150 " pdb=" HG SER A 153 " model vdw 1.543 1.800 nonbonded pdb=" OG SER A 279 " pdb=" HG SER A 409 " model vdw 1.548 1.800 ... (remaining 132967 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 30 15.96 2 O 924 7.97 2 N 799 6.97 2 C 2969 5.97 2 H 4501 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 0.022 4847 Z= 0.189 ANGLE : 0.989 6.777 6597 Z= 0.450 CHIRALITY : 0.045 0.146 709 PLANARITY : 0.004 0.038 852 DIHEDRAL : 11.700 77.068 1719 MIN NONBONDED DISTANCE : 2.214 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.95 RAMACHANDRAN PLOT: OUTLIERS : 0.16 % ALLOWED : 5.26 % FAVORED : 94.57 % ROTAMER: OUTLIERS : 0.57 % ALLOWED : 4.73 % FAVORED : 94.70 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 15.15 % 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: -0.56 (0.33), RESIDUES: 608 HELIX: -2.12 (1.05), RESIDUES: 7 SHEET: 0.02 (0.33), RESIDUES: 223 LOOP : -0.55 (0.32), RESIDUES: 378 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.009 0.001 ARG E 66 TYR 0.009 0.001 TYR A 316 PHE 0.014 0.002 PHE A 410 TRP 0.010 0.001 TRP E 35A HIS 0.005 0.001 HIS A 184 Resolution of map is: 3.2874 Map-model correlation coefficient (CC) CC_mask : 0.8012 weight= None bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 Initial weight estimate from ratio of grad norms: 0.3085413619699749 cycle: 0 start: weight= 0.3085 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.3085 bond: 0.022 angle: 2.49 clash: 8.9 rota: 4.17 rama: f: 84.05 o: 0.33 Z: -3.95 cb: 3.07 shift=0.4543 cc_mask=0.8539 cycle: 1 start: weight= 0.2160 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.2160 bond: 0.018 angle: 2.15 clash: 5.3 rota: 2.84 rama: f: 88.65 o: 0.00 Z: -3.27 cb: 1.08 shift=0.4143 cc_mask=0.8489 cycle: 2 start: weight= 0.1512 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.1512 bond: 0.015 angle: 1.94 clash: 3.0 rota: 1.89 rama: f: 91.12 o: 0.00 Z: -2.63 cb: 0.54 shift=0.3752 cc_mask=0.8438 cycle: 3 start: weight= 0.0756 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.0756 bond: 0.012 angle: 1.72 clash: 1.3 rota: 0.57 rama: f: 94.08 o: 0.00 Z: -1.77 cb: 0.00 shift=0.3031 cc_mask=0.8331 cycle: 4 start: weight= 0.0529 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.0529 bond: 0.011 angle: 1.68 clash: 0.9 rota: 0.38 rama: f: 94.74 o: 0.00 Z: -1.57 cb: 0.00 shift=0.2769 cc_mask=0.8280 cycle: 5 start: weight= 0.0370 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.0370 bond: 0.010 angle: 1.64 clash: 0.5 rota: 0.38 rama: f: 95.07 o: 0.00 Z: -1.40 cb: 0.00 shift=0.2545 cc_mask=0.8228 cycle: 6 start: weight= 0.0185 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.0185 bond: 0.010 angle: 1.62 clash: 0.7 rota: 0.19 rama: f: 95.39 o: 0.00 Z: -1.11 cb: 0.00 shift=0.2304 cc_mask=0.8146 cycle: 7 start: weight= 0.0130 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.0130 bond: 0.010 angle: 1.61 clash: 0.7 rota: 0.19 rama: f: 95.72 o: 0.00 Z: -1.10 cb: 0.00 shift=0.2255 cc_mask=0.8113 cycle: 8 start: weight= 0.0091 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.0091 bond: 0.009 angle: 1.61 clash: 0.7 rota: 0.19 rama: f: 95.72 o: 0.00 Z: -1.07 cb: 0.00 shift=0.2223 cc_mask=0.8087 cycle: 9 start: weight= 0.0045 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.0045 bond: 0.009 angle: 1.61 clash: 0.5 rota: 0.00 rama: f: 95.72 o: 0.00 Z: -1.08 cb: 0.00 shift=0.2184 cc_mask=0.8055 cycle: 10 start: weight= 0.0032 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.0032 bond: 0.009 angle: 1.61 clash: 0.5 rota: 0.00 rama: f: 95.72 o: 0.00 Z: -1.08 cb: 0.00 shift=0.2187 cc_mask=0.8044 cycle: 11 start: weight= 0.0022 bond: 0.004 angle: 0.99 clash: 2.0 rota: 0.57 rama: f: 94.57 o: 0.16 Z: -0.56 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.0022 bond: 0.009 angle: 1.61 clash: 0.5 rota: 0.00 rama: f: 95.72 o: 0.00 Z: -1.08 cb: 0.00 shift=0.2181 cc_mask=0.8036 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0022233494400323425 start: weight= 0.0022 bond: 0.009 angle: 1.61 clash: 0.5 rota: 0.00 rama: f: 95.72 o: 0.00 Z: -1.08 cb: 0.00 shift=0.0000 cc_mask=0.8012 final: weight= 0.0022 bond: 0.009 angle: 1.61 clash: 0.5 rota: 0.00 rama: f: 95.72 o: 0.00 Z: -1.08 cb: 0.00 shift=0.2184 cc_mask=0.8036 start: weight= 0.0022 bond: 0.009 angle: 1.61 clash: 0.5 rota: 0.00 rama: f: 95.72 o: 0.00 Z: -1.08 cb: 0.00 shift=0.2184 cc_mask=0.8036 final: weight= 0.0022 bond: 0.009 angle: 1.58 clash: 0.4 rota: 0.19 rama: f: 95.56 o: 0.00 Z: -1.30 cb: 0.00 shift=0.2920 cc_mask=0.8016 start: weight= 0.0022 bond: 0.009 angle: 1.58 clash: 0.4 rota: 0.19 rama: f: 95.56 o: 0.00 Z: -1.30 cb: 0.00 shift=0.2920 cc_mask=0.8016 final: weight= 0.0022 bond: 0.009 angle: 1.61 clash: 0.4 rota: 0.19 rama: f: 95.89 o: 0.16 Z: -1.36 cb: 0.00 shift=0.3359 cc_mask=0.8006 start: weight= 0.0022 bond: 0.009 angle: 1.61 clash: 0.4 rota: 0.19 rama: f: 95.89 o: 0.16 Z: -1.36 cb: 0.00 shift=0.3359 cc_mask=0.8006 final: weight= 0.0022 bond: 0.009 angle: 1.60 clash: 0.4 rota: 0.00 rama: f: 95.07 o: 0.16 Z: -1.42 cb: 0.00 shift=0.3804 cc_mask=0.7984 start: weight= 0.0022 bond: 0.009 angle: 1.60 clash: 0.4 rota: 0.00 rama: f: 95.07 o: 0.16 Z: -1.42 cb: 0.00 shift=0.3804 cc_mask=0.7984 final: weight= 0.0022 bond: 0.009 angle: 1.61 clash: 0.5 rota: 0.19 rama: f: 94.90 o: 0.16 Z: -1.54 cb: 0.00 shift=0.4123 cc_mask=0.7961 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.032 4847 Z= 0.485 ANGLE : 1.610 9.374 6597 Z= 0.834 CHIRALITY : 0.106 0.374 709 PLANARITY : 0.015 0.178 852 DIHEDRAL : 12.126 114.187 1719 MIN NONBONDED DISTANCE : 2.560 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.54 RAMACHANDRAN PLOT: OUTLIERS : 0.16 % ALLOWED : 4.93 % FAVORED : 94.90 % ROTAMER: OUTLIERS : 0.19 % ALLOWED : 0.95 % FAVORED : 98.86 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 15.15 % 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: -1.54 (0.31), RESIDUES: 608 HELIX: -3.15 (1.11), RESIDUES: 6 SHEET: -1.26 (0.30), RESIDUES: 239 LOOP : -0.73 (0.30), RESIDUES: 363 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.019 0.004 ARG A 219 TYR 0.089 0.018 TYR A 169A PHE 0.054 0.016 PHE A 115 TRP 0.107 0.019 TRP A 361 HIS 0.006 0.002 HIS E 102 Resolution of map is: 3.2874 Map-model correlation coefficient (CC) CC_mask : 0.7961 =============================================================================== Job complete usr+sys time: 1020.44 seconds wall clock time: 18 minutes 11.86 seconds (1091.86 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)