Starting qr.refine on Sun May 19 16:39:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7lkh_23408.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7lkh_23408.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/7lkh_23408.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7lkh_23408.pdb" real_map_files = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7lkh_23408.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/7lkh_23408.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 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 87": "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: 8236 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 4686 Inner-chain residues flagged as termini: ['pdbres="VAL A 72 "', 'pdbres="ARG A 81 "', 'pdbres="GLU A 278 "', 'pdbres="THR A 637 "'] Classifications: {'peptide': 286} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 22, 'TRANS': 263} Chain breaks: 2 Chain: "H" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1865 Classifications: {'peptide': 121} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "L" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1685 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 0.95, per 1000 atoms: 0.12 Number of scatterers: 8236 At special positions: 0 Unit cell: (71.28, 100.44, 84.24, 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 8 16.00 O 788 8.00 N 715 7.00 C 2645 6.00 H 4080 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 1.46 Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Time building geometry restraints manager: 1.69 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: 4079 1.14 - 1.31: 676 1.31 - 1.48: 1790 1.48 - 1.64: 1787 1.64 - 1.81: 9 Bond restraints: 8341 Sorted by residual: bond pdb=" CB PRO A 60 " pdb=" CG PRO A 60 " ideal model delta sigma weight residual 1.492 1.547 -0.055 5.00e-02 4.00e+02 1.23e+00 bond pdb=" C ARG A 696 " pdb=" N HIS A 697 " ideal model delta sigma weight residual 1.329 1.344 -0.015 1.40e-02 5.10e+03 1.18e+00 bond pdb=" C ARG A 267 " pdb=" N GLU A 268 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 1.01e+00 bond pdb=" C VAL H 12 " pdb=" N ARG H 13 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.40e-02 5.10e+03 7.11e-01 bond pdb=" N VAL A 223 " pdb=" CA VAL A 223 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.90e-02 2.77e+03 6.47e-01 ... (remaining 8336 not shown) Histogram of bond angle deviations from ideal: 101.10 - 107.70: 670 107.70 - 114.29: 9525 114.29 - 120.88: 2770 120.88 - 127.48: 2017 127.48 - 134.07: 57 Bond angle restraints: 15039 Sorted by residual: angle pdb=" CA SER A 103 " pdb=" C SER A 103 " pdb=" N PRO A 104 " ideal model delta sigma weight residual 116.90 121.74 -4.84 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C PRO H 41 " pdb=" N GLU H 42 " pdb=" CA GLU H 42 " ideal model delta sigma weight residual 121.70 127.08 -5.38 1.80e+00 3.09e-01 8.94e+00 angle pdb=" CA LEU L 94 " pdb=" C LEU L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 116.90 121.27 -4.37 1.50e+00 4.44e-01 8.49e+00 angle pdb=" CA TRP A 659 " pdb=" C TRP A 659 " pdb=" N PRO A 660 " ideal model delta sigma weight residual 116.90 121.02 -4.12 1.50e+00 4.44e-01 7.53e+00 angle pdb=" C ASP A 83 " pdb=" N TRP A 84 " pdb=" CA TRP A 84 " ideal model delta sigma weight residual 121.70 126.56 -4.86 1.80e+00 3.09e-01 7.29e+00 ... (remaining 15034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 3641 16.26 - 32.52: 217 32.52 - 48.77: 68 48.77 - 65.03: 28 65.03 - 81.29: 8 Dihedral angle restraints: 3962 sinusoidal: 2137 harmonic: 1825 Sorted by residual: dihedral pdb=" CA ARG H 98 " pdb=" C ARG H 98 " pdb=" N TYR H 99 " pdb=" CA TYR H 99 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR L 93 " pdb=" C THR L 93 " pdb=" N LEU L 94 " pdb=" CA LEU L 94 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PRO A 155 " pdb=" C PRO A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 381 0.029 - 0.057: 175 0.057 - 0.086: 32 0.086 - 0.114: 38 0.114 - 0.143: 12 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE A 96 " pdb=" N ILE A 96 " pdb=" C ILE A 96 " pdb=" CB ILE A 96 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL H 93 " pdb=" N VAL H 93 " pdb=" C VAL H 93 " pdb=" CB VAL H 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 635 not shown) Planarity restraints: 1228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 154 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 155 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 155 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 155 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 65 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 66 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 117 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 118 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.018 5.00e-02 4.00e+02 ... (remaining 1225 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 488 2.11 - 2.73: 13139 2.73 - 3.35: 22374 3.35 - 3.98: 30903 3.98 - 4.60: 45361 Nonbonded interactions: 112265 Sorted by model distance: nonbonded pdb="HD22 ASN L 34 " pdb=" O TYR L 49 " model vdw 1.483 1.800 nonbonded pdb=" O SER A 117 " pdb=" HG SER A 120 " model vdw 1.538 1.800 nonbonded pdb=" O GLY A 87 " pdb=" HH TYR A 674 " model vdw 1.572 1.800 nonbonded pdb=" OD2 ASP A 188 " pdb=" HG1 THR A 194 " model vdw 1.590 1.800 nonbonded pdb=" OE1 GLN H 5 " pdb=" H GLN H 5 " model vdw 1.620 1.800 ... (remaining 112260 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 8 15.96 2 O 788 7.97 2 N 715 6.97 2 C 2645 5.97 2 H 4080 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 0.055 4261 Z= 0.190 ANGLE : 0.950 5.415 5799 Z= 0.445 CHIRALITY : 0.042 0.143 638 PLANARITY : 0.004 0.052 746 DIHEDRAL : 12.270 81.289 1562 MIN NONBONDED DISTANCE : 2.298 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 2.80 RAMACHANDRAN PLOT: OUTLIERS : 0.40 % ALLOWED : 6.13 % FAVORED : 93.48 % ROTAMER: OUTLIERS : 0.43 % ALLOWED : 1.74 % FAVORED : 97.83 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % 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: -1.47 (0.36), RESIDUES: 506 HELIX: -0.64 (0.55), RESIDUES: 73 SHEET: -0.68 (0.38), RESIDUES: 161 LOOP : -1.20 (0.38), RESIDUES: 272 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.000 ARG A 652 TYR 0.015 0.001 TYR H 99 PHE 0.010 0.001 PHE A 97 TRP 0.007 0.001 TRP A 84 HIS 0.003 0.001 HIS H 35 Resolution of map is: 2.9854 Map-model correlation coefficient (CC) CC_mask : 0.7466 weight= None bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 Initial weight estimate from ratio of grad norms: 0.2600633824560489 cycle: 0 start: weight= 0.2601 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.2601 bond: 0.023 angle: 2.64 clash: 10.0 rota: 2.17 rama: f: 86.36 o: 2.37 Z: -4.13 cb: 3.69 shift=0.3910 cc_mask=0.7993 cycle: 1 start: weight= 0.1820 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.1820 bond: 0.019 angle: 2.27 clash: 5.1 rota: 1.52 rama: f: 89.13 o: 1.19 Z: -3.57 cb: 1.23 shift=0.3628 cc_mask=0.7923 cycle: 2 start: weight= 0.1274 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.1274 bond: 0.015 angle: 2.02 clash: 3.0 rota: 1.09 rama: f: 91.90 o: 0.99 Z: -2.92 cb: 0.82 shift=0.3275 cc_mask=0.7854 cycle: 3 start: weight= 0.0637 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.0637 bond: 0.012 angle: 1.75 clash: 0.9 rota: 1.30 rama: f: 92.69 o: 0.40 Z: -1.81 cb: 0.82 shift=0.2674 cc_mask=0.7724 cycle: 4 start: weight= 0.0446 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.0446 bond: 0.011 angle: 1.69 clash: 0.4 rota: 1.30 rama: f: 93.87 o: 0.40 Z: -1.38 cb: 0.82 shift=0.2457 cc_mask=0.7662 cycle: 5 start: weight= 0.0312 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.0312 bond: 0.010 angle: 1.65 clash: 0.2 rota: 0.43 rama: f: 93.87 o: 0.40 Z: -1.12 cb: 0.82 shift=0.2281 cc_mask=0.7605 cycle: 6 start: weight= 0.0156 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.0156 bond: 0.010 angle: 1.62 clash: 0.2 rota: 0.43 rama: f: 94.66 o: 0.40 Z: -0.96 cb: 0.61 shift=0.2166 cc_mask=0.7526 cycle: 7 start: weight= 0.0109 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.0109 bond: 0.009 angle: 1.62 clash: 0.2 rota: 0.43 rama: f: 94.27 o: 0.20 Z: -0.92 cb: 0.61 shift=0.2155 cc_mask=0.7496 cycle: 8 start: weight= 0.0076 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.0076 bond: 0.009 angle: 1.62 clash: 0.1 rota: 0.43 rama: f: 94.27 o: 0.20 Z: -0.91 cb: 0.61 shift=0.2160 cc_mask=0.7473 cycle: 9 start: weight= 0.0038 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.0038 bond: 0.009 angle: 1.62 clash: 0.4 rota: 0.43 rama: f: 94.47 o: 0.20 Z: -0.92 cb: 0.61 shift=0.2160 cc_mask=0.7446 cycle: 10 start: weight= 0.0027 bond: 0.004 angle: 0.95 clash: 2.8 rota: 0.43 rama: f: 93.48 o: 0.40 Z: -1.47 cb: 0.00 shift=0.0000 cc_mask=0.7466 final: weight= 0.0027 bond: 0.009 angle: 1.62 clash: 0.4 rota: 0.43 rama: f: 94.47 o: 0.20 Z: -0.92 cb: 0.82 shift=0.2179 cc_mask=0.7435 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.0026771672272250238 start: weight= 0.0027 bond: 0.009 angle: 1.62 clash: 0.4 rota: 0.43 rama: f: 94.47 o: 0.20 Z: -0.92 cb: 0.82 shift=0.0000 cc_mask=0.7466 final: weight= 0.0027 bond: 0.009 angle: 1.62 clash: 0.4 rota: 0.43 rama: f: 94.47 o: 0.20 Z: -0.93 cb: 0.61 shift=0.2180 cc_mask=0.7435 start: weight= 0.0027 bond: 0.009 angle: 1.62 clash: 0.4 rota: 0.43 rama: f: 94.47 o: 0.20 Z: -0.93 cb: 0.61 shift=0.2180 cc_mask=0.7435 final: weight= 0.0027 bond: 0.009 angle: 1.57 clash: 0.4 rota: 0.43 rama: f: 94.86 o: 0.20 Z: -1.07 cb: 0.41 shift=0.2864 cc_mask=0.7400 start: weight= 0.0027 bond: 0.009 angle: 1.57 clash: 0.4 rota: 0.43 rama: f: 94.86 o: 0.20 Z: -1.07 cb: 0.41 shift=0.2864 cc_mask=0.7400 final: weight= 0.0027 bond: 0.009 angle: 1.60 clash: 0.4 rota: 0.87 rama: f: 94.66 o: 0.20 Z: -1.27 cb: 0.20 shift=0.3468 cc_mask=0.7358 start: weight= 0.0027 bond: 0.009 angle: 1.60 clash: 0.4 rota: 0.87 rama: f: 94.66 o: 0.20 Z: -1.27 cb: 0.20 shift=0.3468 cc_mask=0.7358 final: weight= 0.0027 bond: 0.009 angle: 1.59 clash: 0.6 rota: 0.65 rama: f: 94.86 o: 0.20 Z: -1.35 cb: 0.41 shift=0.3992 cc_mask=0.7318 start: weight= 0.0027 bond: 0.009 angle: 1.59 clash: 0.6 rota: 0.65 rama: f: 94.86 o: 0.20 Z: -1.35 cb: 0.41 shift=0.3992 cc_mask=0.7318 final: weight= 0.0027 bond: 0.009 angle: 1.61 clash: 0.6 rota: 0.65 rama: f: 95.06 o: 0.20 Z: -1.50 cb: 0.41 shift=0.4282 cc_mask=0.7293 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.009 0.033 4261 Z= 0.495 ANGLE : 1.606 9.853 5799 Z= 0.835 CHIRALITY : 0.116 0.463 638 PLANARITY : 0.019 0.128 746 DIHEDRAL : 13.339 85.635 1562 MIN NONBONDED DISTANCE : 2.574 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.61 RAMACHANDRAN PLOT: OUTLIERS : 0.20 % ALLOWED : 4.74 % FAVORED : 95.06 % ROTAMER: OUTLIERS : 0.65 % ALLOWED : 2.39 % FAVORED : 96.96 % CBETA DEVIATIONS : 0.41 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % 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: -1.50 (0.35), RESIDUES: 506 HELIX: -1.99 (0.40), RESIDUES: 80 SHEET: -1.35 (0.38), RESIDUES: 154 LOOP : -0.27 (0.37), RESIDUES: 272 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.021 0.004 ARG H 98 TYR 0.159 0.024 TYR L 32 PHE 0.033 0.008 PHE L 98 TRP 0.082 0.024 TRP A 659 HIS 0.008 0.002 HIS H 35 Resolution of map is: 2.9854 Map-model correlation coefficient (CC) CC_mask : 0.7293 =============================================================================== Job complete usr+sys time: 789.92 seconds wall clock time: 14 minutes 11.33 seconds (851.33 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)