Starting qr.refine on Sun May 19 17:24:12 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8aza_15757.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8aza_15757.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/8aza_15757.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8aza_15757.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8aza_15757.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/8aza_15757.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 "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 283": "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: 9986 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1205 Classifications: {'peptide': 76} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "A" Number of atoms: 4697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4697 Inner-chain residues flagged as termini: ['pdbres="LEU A 175 "', 'pdbres="THR A 189 "', 'pdbres="ASN A 197 "', 'pdbres="ARG A 205 "', 'pdbres="GLU A 230 "', 'pdbres="ASN A 234 "'] Classifications: {'peptide': 284} Modifications used: {'COO': 4, 'NH3': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 263} Chain breaks: 3 Chain: "B" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 4084 Inner-chain residues flagged as termini: ['pdbres="LEU B 49 "', 'pdbres="GLU B 59 "', 'pdbres="ARG B 171 "', 'pdbres="ALA B 206 "', 'pdbres="PRO B 228 "', 'pdbres="ARG B 247 "'] Classifications: {'peptide': 246} Modifications used: {'COO': 4, 'NH3': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 229} Chain breaks: 3 Time building chain proxies: 1.17, per 1000 atoms: 0.12 Number of scatterers: 9986 At special positions: 0 Unit cell: (72.776, 76.911, 96.759, 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 20 16.00 O 882 8.00 N 872 7.00 C 3204 6.00 H 5008 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: 1.81 Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Time building geometry restraints manager: 2.08 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: 4999 1.14 - 1.31: 805 1.31 - 1.48: 2082 1.48 - 1.65: 2202 1.65 - 1.82: 31 Bond restraints: 10119 Sorted by residual: bond pdb=" C ALA B 9 " pdb=" N LEU B 10 " ideal model delta sigma weight residual 1.329 1.360 -0.031 1.40e-02 5.10e+03 4.97e+00 bond pdb=" CB LYS B 61 " pdb=" CG LYS B 61 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.36e-01 bond pdb=" C SER B 29 " pdb=" N GLY B 30 " ideal model delta sigma weight residual 1.329 1.317 0.012 1.40e-02 5.10e+03 7.06e-01 bond pdb=" C HIS A 145 " pdb=" N ASP A 146 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.40e-02 5.10e+03 6.60e-01 bond pdb=" CB PRO A 256 " pdb=" CG PRO A 256 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.12e-01 ... (remaining 10114 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.39: 625 107.39 - 114.05: 11788 114.05 - 120.71: 3367 120.71 - 127.37: 2466 127.37 - 134.03: 93 Bond angle restraints: 18339 Sorted by residual: angle pdb=" CA GLU B 291 " pdb=" C GLU B 291 " pdb=" N PRO B 292 " ideal model delta sigma weight residual 116.90 121.82 -4.92 1.50e+00 4.44e-01 1.07e+01 angle pdb=" CA GLU A 291 " pdb=" C GLU A 291 " pdb=" N PRO A 292 " ideal model delta sigma weight residual 116.90 121.32 -4.42 1.50e+00 4.44e-01 8.67e+00 angle pdb=" CA TRP A 118 " pdb=" C TRP A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 116.90 120.60 -3.70 1.50e+00 4.44e-01 6.08e+00 angle pdb=" CA TRP A 118 " pdb=" CB TRP A 118 " pdb=" CG TRP A 118 " ideal model delta sigma weight residual 113.60 117.81 -4.21 1.90e+00 2.77e-01 4.92e+00 angle pdb=" C VAL A 217 " pdb=" N ILE A 218 " pdb=" CA ILE A 218 " ideal model delta sigma weight residual 121.70 117.71 3.99 1.80e+00 3.09e-01 4.91e+00 ... (remaining 18334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4198 17.81 - 35.62: 378 35.62 - 53.44: 135 53.44 - 71.25: 31 71.25 - 89.06: 6 Dihedral angle restraints: 4748 sinusoidal: 2580 harmonic: 2168 Sorted by residual: dihedral pdb=" CA PRO B 281 " pdb=" C PRO B 281 " pdb=" N SER B 282 " pdb=" CA SER B 282 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET A 98 " pdb=" C MET A 98 " pdb=" N PRO A 99 " pdb=" CA PRO A 99 " ideal model delta harmonic sigma weight residual -180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA HIS A 159 " pdb=" C HIS A 159 " pdb=" N VAL A 160 " pdb=" CA VAL A 160 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 4745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 453 0.029 - 0.057: 207 0.057 - 0.086: 52 0.086 - 0.114: 38 0.114 - 0.143: 9 Chirality restraints: 759 Sorted by residual: chirality pdb=" CA ILE B 78 " pdb=" N ILE B 78 " pdb=" C ILE B 78 " pdb=" CB ILE B 78 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA VAL B 116 " pdb=" N VAL B 116 " pdb=" C VAL B 116 " pdb=" CB VAL B 116 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE A 81 " pdb=" N ILE A 81 " pdb=" C ILE A 81 " pdb=" CB ILE A 81 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 756 not shown) Planarity restraints: 1443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 280 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO B 281 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 180 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO C 181 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 53 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 54 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " 0.021 5.00e-02 4.00e+02 ... (remaining 1440 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 574 2.03 - 2.67: 13967 2.67 - 3.31: 30979 3.31 - 3.96: 40449 3.96 - 4.60: 59000 Nonbonded interactions: 144969 Sorted by model distance: nonbonded pdb=" H ALA B 19 " pdb=" O ARG B 36 " model vdw 1.384 1.800 nonbonded pdb=" O LEU A 153 " pdb=" H LYS A 161 " model vdw 1.414 1.800 nonbonded pdb=" O ASN A 234 " pdb="HE21 GLN A 237 " model vdw 1.425 1.800 nonbonded pdb=" O GLU B 221 " pdb=" H ARG B 225 " model vdw 1.467 1.800 nonbonded pdb=" H LEU A 153 " pdb=" O LYS A 161 " model vdw 1.486 1.800 ... (remaining 144964 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 20 15.96 2 O 882 7.97 2 N 872 6.97 2 C 3204 5.97 2 H 5008 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 0.039 5111 Z= 0.194 ANGLE : 0.975 5.908 6939 Z= 0.460 CHIRALITY : 0.040 0.143 759 PLANARITY : 0.005 0.047 886 DIHEDRAL : 16.129 78.514 1916 MIN NONBONDED DISTANCE : 2.109 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 7.64 RAMACHANDRAN PLOT: OUTLIERS : 0.17 % ALLOWED : 5.78 % FAVORED : 94.05 % ROTAMER: OUTLIERS : 1.65 % ALLOWED : 20.92 % FAVORED : 77.43 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 5.00 % 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: -1.94 (0.31), RESIDUES: 588 HELIX: -1.37 (0.29), RESIDUES: 244 SHEET: -2.56 (0.61), RESIDUES: 55 LOOP : -0.77 (0.33), RESIDUES: 289 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.004 0.001 ARG B 225 TYR 0.009 0.001 TYR C 191 PHE 0.012 0.001 PHE A 229 TRP 0.014 0.001 TRP A 118 HIS 0.002 0.001 HIS A 16 Resolution of map is: 4.3185 Map-model correlation coefficient (CC) CC_mask : 0.6679 weight= None bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 Initial weight estimate from ratio of grad norms: 0.6146420020749539 cycle: 0 start: weight= 0.6146 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.6146 bond: 0.028 angle: 3.33 clash: 142.9 rota: 14.68 rama: f: 73.30 o: 6.12 Z: -6.71 cb: 8.06 shift=0.8201 cc_mask=0.7618 cycle: 1 start: weight= 0.4302 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.4302 bond: 0.022 angle: 2.80 clash: 87.9 rota: 11.56 rama: f: 80.95 o: 3.40 Z: -6.19 cb: 2.57 shift=0.7345 cc_mask=0.7523 cycle: 2 start: weight= 0.3012 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.3012 bond: 0.018 angle: 2.42 clash: 49.1 rota: 8.26 rama: f: 86.39 o: 1.53 Z: -5.58 cb: 0.69 shift=0.6068 cc_mask=0.7406 cycle: 3 start: weight= 0.1506 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.1506 bond: 0.013 angle: 1.99 clash: 14.9 rota: 3.85 rama: f: 92.69 o: 0.51 Z: -4.09 cb: 0.51 shift=0.4166 cc_mask=0.7161 cycle: 4 start: weight= 0.1054 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.1054 bond: 0.012 angle: 1.87 clash: 7.9 rota: 2.94 rama: f: 94.39 o: 0.34 Z: -3.52 cb: 0.34 shift=0.3485 cc_mask=0.7035 cycle: 5 start: weight= 0.0738 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.0738 bond: 0.011 angle: 1.80 clash: 4.6 rota: 2.94 rama: f: 95.58 o: 0.34 Z: -3.06 cb: 0.34 shift=0.2985 cc_mask=0.6923 cycle: 6 start: weight= 0.0369 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.0369 bond: 0.010 angle: 1.75 clash: 1.9 rota: 2.39 rama: f: 95.92 o: 0.34 Z: -2.74 cb: 0.34 shift=0.2629 cc_mask=0.6765 cycle: 7 start: weight= 0.0258 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.0258 bond: 0.009 angle: 1.74 clash: 1.5 rota: 2.20 rama: f: 95.92 o: 0.34 Z: -2.77 cb: 0.34 shift=0.2549 cc_mask=0.6709 cycle: 8 start: weight= 0.0181 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.0181 bond: 0.009 angle: 1.74 clash: 1.4 rota: 2.20 rama: f: 96.60 o: 0.34 Z: -2.74 cb: 0.34 shift=0.2571 cc_mask=0.6664 cycle: 9 start: weight= 0.0090 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.0090 bond: 0.009 angle: 1.74 clash: 1.0 rota: 2.39 rama: f: 96.43 o: 0.34 Z: -2.67 cb: 0.34 shift=0.2610 cc_mask=0.6606 cycle: 10 start: weight= 0.0063 bond: 0.004 angle: 0.97 clash: 7.6 rota: 1.65 rama: f: 94.05 o: 0.17 Z: -1.94 cb: 0.00 shift=0.0000 cc_mask=0.6679 final: weight= 0.0063 bond: 0.009 angle: 1.73 clash: 0.9 rota: 2.39 rama: f: 96.60 o: 0.34 Z: -2.67 cb: 0.34 shift=0.2651 cc_mask=0.6587 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0063273014789351715 start: weight= 0.0063 bond: 0.009 angle: 1.73 clash: 0.9 rota: 2.39 rama: f: 96.60 o: 0.34 Z: -2.67 cb: 0.34 shift=0.0000 cc_mask=0.6679 final: weight= 0.0063 bond: 0.009 angle: 1.73 clash: 0.9 rota: 2.39 rama: f: 96.60 o: 0.34 Z: -2.66 cb: 0.34 shift=0.2621 cc_mask=0.6588 start: weight= 0.0063 bond: 0.009 angle: 1.73 clash: 0.9 rota: 2.39 rama: f: 96.60 o: 0.34 Z: -2.66 cb: 0.34 shift=0.2621 cc_mask=0.6588 final: weight= 0.0063 bond: 0.009 angle: 1.68 clash: 1.4 rota: 2.20 rama: f: 96.43 o: 0.17 Z: -2.84 cb: 0.17 shift=0.3500 cc_mask=0.6543 start: weight= 0.0063 bond: 0.009 angle: 1.68 clash: 1.4 rota: 2.20 rama: f: 96.43 o: 0.17 Z: -2.84 cb: 0.17 shift=0.3500 cc_mask=0.6543 final: weight= 0.0063 bond: 0.009 angle: 1.71 clash: 1.4 rota: 2.75 rama: f: 96.94 o: 0.17 Z: -2.85 cb: 0.34 shift=0.4139 cc_mask=0.6499 start: weight= 0.0063 bond: 0.009 angle: 1.71 clash: 1.4 rota: 2.75 rama: f: 96.94 o: 0.17 Z: -2.85 cb: 0.34 shift=0.4139 cc_mask=0.6499 final: weight= 0.0063 bond: 0.009 angle: 1.69 clash: 1.9 rota: 2.20 rama: f: 96.43 o: 0.17 Z: -2.94 cb: 0.17 shift=0.4675 cc_mask=0.6471 start: weight= 0.0063 bond: 0.009 angle: 1.69 clash: 1.9 rota: 2.20 rama: f: 96.43 o: 0.17 Z: -2.94 cb: 0.17 shift=0.4675 cc_mask=0.6471 final: weight= 0.0063 bond: 0.009 angle: 1.70 clash: 1.5 rota: 2.02 rama: f: 96.26 o: 0.34 Z: -2.81 cb: 0.17 shift=0.5202 cc_mask=0.6438 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.038 5111 Z= 0.491 ANGLE : 1.696 9.276 6939 Z= 0.915 CHIRALITY : 0.131 0.513 759 PLANARITY : 0.018 0.164 886 DIHEDRAL : 15.399 159.070 1916 MIN NONBONDED DISTANCE : 2.574 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.51 RAMACHANDRAN PLOT: OUTLIERS : 0.34 % ALLOWED : 3.40 % FAVORED : 96.26 % ROTAMER: OUTLIERS : 2.02 % ALLOWED : 11.74 % FAVORED : 86.24 % CBETA DEVIATIONS : 0.17 % PEPTIDE PLANE: CIS-PROLINE : 5.00 % 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: -2.81 (0.29), RESIDUES: 588 HELIX: -2.25 (0.24), RESIDUES: 236 SHEET: -3.12 (0.51), RESIDUES: 67 LOOP : -0.99 (0.33), RESIDUES: 285 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.024 0.004 ARG C 166 TYR 0.130 0.016 TYR A 113 PHE 0.048 0.010 PHE C 170 TRP 0.091 0.022 TRP B 40 HIS 0.006 0.002 HIS B 159 Resolution of map is: 4.3185 Map-model correlation coefficient (CC) CC_mask : 0.6438 =============================================================================== Job complete usr+sys time: 954.14 seconds wall clock time: 17 minutes 7.49 seconds (1027.49 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)