Starting qr.refine on Sun May 19 13:57:54 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5xb1_6714.map Found model, /net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5xb1_6714.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/5xb1_6714.map" default_real_map = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5xb1_6714.map" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5xb1_6714.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/cryoem_cp/regularized/5xb1_6714.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: 2522 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2522 Classifications: {'peptide': 155} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Time building chain proxies: 0.39, per 1000 atoms: 0.15 Number of scatterers: 2522 At special positions: 0 Unit cell: (65.673, 58.687, 65.673, 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 7 16.00 O 247 8.00 N 228 7.00 C 802 6.00 H 1238 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: 0.40 Adding C-beta torsion restraints... Number of C-beta restraints generated: 300 Time building geometry restraints manager: 0.47 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: 1235 1.14 - 1.31: 230 1.31 - 1.48: 512 1.48 - 1.64: 559 1.64 - 1.81: 11 Bond restraints: 2547 Sorted by residual: bond pdb=" CA ASN A 126 " pdb=" C ASN A 126 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.10e-02 2.27e+03 9.74e-01 bond pdb=" C GLU A 62 " pdb=" O GLU A 62 " ideal model delta sigma weight residual 1.231 1.250 -0.019 2.00e-02 2.50e+03 9.12e-01 bond pdb=" C ASN A 110 " pdb=" O ASN A 110 " ideal model delta sigma weight residual 1.231 1.246 -0.015 2.00e-02 2.50e+03 5.33e-01 bond pdb=" C TYR A 55 " pdb=" N PHE A 56 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.40e-02 5.10e+03 4.60e-01 bond pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta sigma weight residual 1.466 1.476 -0.010 1.50e-02 4.44e+03 4.49e-01 ... (remaining 2542 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.85: 30 106.85 - 113.61: 2943 113.61 - 120.37: 869 120.37 - 127.13: 726 127.13 - 133.89: 13 Bond angle restraints: 4581 Sorted by residual: angle pdb=" N LEU A 49 " pdb=" CA LEU A 49 " pdb=" C LEU A 49 " ideal model delta sigma weight residual 111.00 106.47 4.53 2.80e+00 1.28e-01 2.61e+00 angle pdb=" CA HIS A 137 " pdb=" C HIS A 137 " pdb=" N TYR A 138 " ideal model delta sigma weight residual 116.20 119.41 -3.21 2.00e+00 2.50e-01 2.57e+00 angle pdb=" C GLU A 65 " pdb=" N HIS A 66 " pdb=" CA HIS A 66 " ideal model delta sigma weight residual 121.70 119.00 2.70 1.80e+00 3.09e-01 2.24e+00 angle pdb=" N ILE A 86 " pdb=" CA ILE A 86 " pdb=" C ILE A 86 " ideal model delta sigma weight residual 111.00 106.97 4.03 2.80e+00 1.28e-01 2.07e+00 angle pdb=" C ASN A 155 " pdb=" N LEU A 156 " pdb=" CA LEU A 156 " ideal model delta sigma weight residual 121.70 119.14 2.56 1.80e+00 3.09e-01 2.02e+00 ... (remaining 4576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 1137 16.71 - 33.41: 34 33.41 - 50.12: 15 50.12 - 66.83: 2 66.83 - 83.53: 4 Dihedral angle restraints: 1192 sinusoidal: 640 harmonic: 552 Sorted by residual: dihedral pdb=" CA HIS A 137 " pdb=" C HIS A 137 " pdb=" N TYR A 138 " pdb=" CA TYR A 138 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP A 151 " pdb=" C ASP A 151 " pdb=" N HIS A 152 " pdb=" CA HIS A 152 " ideal model delta harmonic sigma weight residual 180.00 164.89 15.11 0 5.00e+00 4.00e-02 9.14e+00 dihedral pdb=" CA VAL A 47 " pdb=" C VAL A 47 " pdb=" N ALA A 48 " pdb=" CA ALA A 48 " ideal model delta harmonic sigma weight residual 180.00 167.53 12.47 0 5.00e+00 4.00e-02 6.22e+00 ... (remaining 1189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 121 0.024 - 0.049: 44 0.049 - 0.073: 11 0.073 - 0.097: 6 0.097 - 0.121: 3 Chirality restraints: 185 Sorted by residual: chirality pdb=" CA ILE A 86 " pdb=" N ILE A 86 " pdb=" C ILE A 86 " pdb=" CB ILE A 86 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA VAL A 47 " pdb=" N VAL A 47 " pdb=" C VAL A 47 " pdb=" CB VAL A 47 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-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 2.54 -0.11 2.00e-01 2.50e+01 2.77e-01 ... (remaining 182 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 127 " 0.012 5.00e-02 4.00e+02 1.88e-02 5.65e-01 pdb=" N PRO A 128 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 128 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 128 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 88 " -0.012 5.00e-02 4.00e+02 1.76e-02 4.94e-01 pdb=" N PRO A 89 " 0.030 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 28 " -0.003 2.00e-02 2.50e+03 6.39e-03 4.08e-01 pdb=" C GLU A 28 " 0.011 2.00e-02 2.50e+03 pdb=" O GLU A 28 " -0.004 2.00e-02 2.50e+03 pdb=" N LEU A 29 " -0.004 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.32: 396 2.32 - 2.89: 5445 2.89 - 3.46: 6421 3.46 - 4.03: 8126 4.03 - 4.60: 12102 Nonbonded interactions: 32490 Sorted by model distance: nonbonded pdb=" OD1 ASP A 92 " pdb=" H ASP A 93 " model vdw 1.744 1.800 nonbonded pdb=" O ASP A 132 " pdb=" HG1 THR A 136 " model vdw 1.765 1.800 nonbonded pdb=" O SER A 32 " pdb=" HG SER A 60 " model vdw 1.778 1.800 nonbonded pdb=" H GLN A 15 " pdb=" HG2 GLN A 15 " model vdw 1.820 2.170 nonbonded pdb=" HH TYR A 35 " pdb=" OE2 GLU A 108 " model vdw 1.843 1.800 ... (remaining 32485 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 7 15.96 2 O 247 7.97 2 N 228 6.97 2 C 802 5.97 2 H 1238 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 0.021 1309 Z= 0.227 ANGLE : 0.844 4.527 1762 Z= 0.426 CHIRALITY : 0.032 0.121 185 PLANARITY : 0.003 0.019 233 DIHEDRAL : 11.226 83.533 496 MIN NONBONDED DISTANCE : 2.205 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 1.19 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.96 % FAVORED : 98.04 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.00 % FAVORED : 100.00 % 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: 0.23 (0.63), RESIDUES: 153 HELIX: 0.88 (0.44), RESIDUES: 117 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -2.19 (0.91), RESIDUES: 36 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.002 0.000 ARG A 10 TYR 0.010 0.001 TYR A 33 PHE 0.005 0.001 PHE A 133 TRP 0.005 0.001 TRP A 94 HIS 0.002 0.001 HIS A 137 Resolution of map is: 3.0633 Map-model correlation coefficient (CC) CC_mask : 0.8393 weight= None bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 Initial weight estimate from ratio of grad norms: 0.3318326948635972 cycle: 0 start: weight= 0.3318 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.3318 bond: 0.020 angle: 2.28 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -5.55 cb: 0.00 shift=0.2427 cc_mask=0.8673 cycle: 1 start: weight= 0.2323 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.2323 bond: 0.016 angle: 1.97 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -4.70 cb: 0.00 shift=0.2354 cc_mask=0.8662 cycle: 2 start: weight= 0.1626 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.1626 bond: 0.013 angle: 1.75 clash: 0.4 rota: 0.00 rama: f: 97.39 o: 0.00 Z: -3.52 cb: 0.00 shift=0.2221 cc_mask=0.8642 cycle: 3 start: weight= 0.0813 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0813 bond: 0.010 angle: 1.51 clash: 0.4 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -1.41 cb: 0.67 shift=0.2288 cc_mask=0.8605 cycle: 4 start: weight= 0.0569 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0569 bond: 0.010 angle: 1.45 clash: 0.4 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -0.64 cb: 0.67 shift=0.2164 cc_mask=0.8573 cycle: 5 start: weight= 0.0398 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0398 bond: 0.009 angle: 1.42 clash: 0.0 rota: 0.00 rama: f: 98.04 o: 0.00 Z: -0.14 cb: 0.00 shift=0.2051 cc_mask=0.8541 cycle: 6 start: weight= 0.0199 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0199 bond: 0.009 angle: 1.39 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.51 cb: 0.00 shift=0.1842 cc_mask=0.8484 cycle: 7 start: weight= 0.0139 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0139 bond: 0.009 angle: 1.38 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.80 cb: 0.00 shift=0.1848 cc_mask=0.8462 cycle: 8 start: weight= 0.0098 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0098 bond: 0.008 angle: 1.38 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.87 cb: 0.00 shift=0.1841 cc_mask=0.8444 cycle: 9 start: weight= 0.0049 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0049 bond: 0.008 angle: 1.38 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.91 cb: 0.00 shift=0.1835 cc_mask=0.8416 cycle: 10 start: weight= 0.0034 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0034 bond: 0.008 angle: 1.38 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.93 cb: 0.00 shift=0.1807 cc_mask=0.8407 cycle: 11 start: weight= 0.0024 bond: 0.004 angle: 0.84 clash: 1.2 rota: 0.00 rama: f: 98.04 o: 0.00 Z: 0.23 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0024 bond: 0.008 angle: 1.38 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.87 cb: 0.00 shift=0.1806 cc_mask=0.8402 <<<<< weight optimization stalled: quitting >>>>> Using last weight to continue: 0.002391186813977951 start: weight= 0.0024 bond: 0.008 angle: 1.38 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.87 cb: 0.00 shift=0.0000 cc_mask=0.8393 final: weight= 0.0024 bond: 0.008 angle: 1.38 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.88 cb: 0.00 shift=0.1783 cc_mask=0.8402 start: weight= 0.0024 bond: 0.008 angle: 1.38 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.88 cb: 0.00 shift=0.1783 cc_mask=0.8402 final: weight= 0.0024 bond: 0.008 angle: 1.37 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.05 cb: 0.00 shift=0.2741 cc_mask=0.8354 start: weight= 0.0024 bond: 0.008 angle: 1.37 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: 0.05 cb: 0.00 shift=0.2741 cc_mask=0.8354 final: weight= 0.0024 bond: 0.008 angle: 1.37 clash: 0.0 rota: 0.00 rama: f: 99.35 o: 0.00 Z: -0.22 cb: 0.00 shift=0.3301 cc_mask=0.8300 start: weight= 0.0024 bond: 0.008 angle: 1.37 clash: 0.0 rota: 0.00 rama: f: 99.35 o: 0.00 Z: -0.22 cb: 0.00 shift=0.3301 cc_mask=0.8300 final: weight= 0.0024 bond: 0.008 angle: 1.37 clash: 0.0 rota: 0.00 rama: f: 99.35 o: 0.00 Z: -0.80 cb: 0.67 shift=0.4054 cc_mask=0.8201 start: weight= 0.0024 bond: 0.008 angle: 1.37 clash: 0.0 rota: 0.00 rama: f: 99.35 o: 0.00 Z: -0.80 cb: 0.67 shift=0.4054 cc_mask=0.8201 final: weight= 0.0024 bond: 0.008 angle: 1.37 clash: 0.0 rota: 0.00 rama: f: 98.69 o: 0.00 Z: -1.09 cb: 0.67 shift=0.4412 cc_mask=0.8146 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY DEVIATIONS FROM IDEAL VALUES - RMSD, RMSZ FOR BONDS AND ANGLES. BOND : 0.008 0.031 1309 Z= 0.472 ANGLE : 1.368 9.394 1762 Z= 0.786 CHIRALITY : 0.102 0.448 185 PLANARITY : 0.013 0.091 233 DIHEDRAL : 12.522 88.066 496 MIN NONBONDED DISTANCE : 2.611 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 0.00 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 1.31 % FAVORED : 98.69 % ROTAMER: OUTLIERS : 0.00 % ALLOWED : 0.71 % FAVORED : 99.29 % CBETA DEVIATIONS : 0.67 % 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: -1.09 (0.57), RESIDUES: 153 HELIX: -0.89 (0.35), RESIDUES: 124 SHEET: NONE (NONE), RESIDUES: 0 LOOP : 1.09 (1.30), RESIDUES: 29 MAX DEVIATION FROM PLANES: TYPE MAXDEV MEANDEV LINEINFILE ARG 0.016 0.004 ARG A 44 TYR 0.057 0.017 TYR A 33 PHE 0.054 0.014 PHE A 42 TRP 0.048 0.021 TRP A 94 HIS 0.007 0.002 HIS A 129 Resolution of map is: 3.0633 Map-model correlation coefficient (CC) CC_mask : 0.8146 =============================================================================== Job complete usr+sys time: 294.67 seconds wall clock time: 5 minutes 35.64 seconds (335.64 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)