Starting phenix.real_space_refine on Tue Feb 3 12:39:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xbl_66704/02_2026/9xbl_66704.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xbl_66704/02_2026/9xbl_66704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xbl_66704/02_2026/9xbl_66704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xbl_66704/02_2026/9xbl_66704.map" model { file = "/net/cci-nas-00/data/ceres_data/9xbl_66704/02_2026/9xbl_66704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xbl_66704/02_2026/9xbl_66704.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1385 2.51 5 N 445 2.21 5 O 475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2305 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 461 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.24, per 1000 atoms: 0.10 Number of scatterers: 2305 At special positions: 0 Unit cell: (66.4, 63.91, 43.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 475 8.00 N 445 7.00 C 1385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.17 Conformation dependent library (CDL) restraints added in 86.0 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 460 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 57.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 8 through 16 removed outlier: 6.531A pdb=" N ASN B 9 " --> pdb=" O GLN D 10 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASN D 12 " --> pdb=" O ASN B 9 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN B 11 " --> pdb=" O ASN D 12 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLN D 14 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR B 13 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N TYR D 16 " --> pdb=" O TYR B 13 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN B 15 " --> pdb=" O TYR D 16 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN A 9 " --> pdb=" O GLN B 10 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASN B 12 " --> pdb=" O ASN A 9 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN A 11 " --> pdb=" O ASN B 12 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLN B 14 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR A 13 " --> pdb=" O GLN B 14 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N TYR B 16 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN A 15 " --> pdb=" O TYR B 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 39 removed outlier: 8.989A pdb=" N ARG B 28 " --> pdb=" O TYR D 29 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N GLY D 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN B 30 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLN D 33 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR B 32 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N TYR D 35 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA B 34 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA D 37 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ASN B 36 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 10.001A pdb=" N ALA D 39 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N GLN B 38 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N ARG A 28 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N GLY B 31 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN A 30 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLN B 33 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR A 32 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR B 35 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA A 34 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA B 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ASN A 36 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N ALA B 39 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N GLN A 38 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR A 29 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN C 30 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY A 31 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 37 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN C 38 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 39 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N TYR C 29 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN E 30 " --> pdb=" O TYR C 29 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY C 31 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA C 37 " --> pdb=" O ASN E 36 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLN E 38 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA C 39 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 45 through 57 removed outlier: 6.188A pdb=" N TYR A 46 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TYR C 49 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN A 48 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLY C 51 " --> pdb=" O ASN A 48 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN A 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N SER C 53 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR A 52 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N TYR C 55 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY A 54 " --> pdb=" O TYR C 55 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLN C 57 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLN A 56 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR C 46 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR E 49 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN C 48 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLY E 51 " --> pdb=" O ASN C 48 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN C 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER E 53 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR C 52 " --> pdb=" O SER E 53 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N TYR E 55 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY C 54 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLN E 57 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN C 56 " --> pdb=" O GLN E 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 60 through 61 removed outlier: 6.332A pdb=" N TYR B 60 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR A 60 " --> pdb=" O GLN B 61 " (cutoff:3.500A) 52 hydrogen bonds defined for protein. 156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.19 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 415 1.29 - 1.35: 440 1.35 - 1.41: 385 1.41 - 1.48: 290 1.48 - 1.54: 830 Bond restraints: 2360 Sorted by residual: bond pdb=" N ASN A 12 " pdb=" CA ASN A 12 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.91e+00 bond pdb=" N TYR A 16 " pdb=" CA TYR A 16 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.90e+00 bond pdb=" N TYR E 16 " pdb=" CA TYR E 16 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.86e+00 bond pdb=" N TYR D 16 " pdb=" CA TYR D 16 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.86e+00 bond pdb=" N ASN B 12 " pdb=" CA ASN B 12 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.79e+00 ... (remaining 2355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 2737 1.15 - 2.30: 213 2.30 - 3.45: 115 3.45 - 4.60: 75 4.60 - 5.75: 40 Bond angle restraints: 3180 Sorted by residual: angle pdb=" N TYR B 16 " pdb=" CA TYR B 16 " pdb=" C TYR B 16 " ideal model delta sigma weight residual 108.34 114.09 -5.75 1.64e+00 3.72e-01 1.23e+01 angle pdb=" N TYR E 16 " pdb=" CA TYR E 16 " pdb=" C TYR E 16 " ideal model delta sigma weight residual 108.34 114.08 -5.74 1.64e+00 3.72e-01 1.23e+01 angle pdb=" N TYR C 16 " pdb=" CA TYR C 16 " pdb=" C TYR C 16 " ideal model delta sigma weight residual 108.34 114.07 -5.73 1.64e+00 3.72e-01 1.22e+01 angle pdb=" N TYR D 16 " pdb=" CA TYR D 16 " pdb=" C TYR D 16 " ideal model delta sigma weight residual 108.34 114.06 -5.72 1.64e+00 3.72e-01 1.22e+01 angle pdb=" N TYR A 16 " pdb=" CA TYR A 16 " pdb=" C TYR A 16 " ideal model delta sigma weight residual 108.34 114.04 -5.70 1.64e+00 3.72e-01 1.21e+01 ... (remaining 3175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 1170 17.65 - 35.31: 95 35.31 - 52.96: 35 52.96 - 70.62: 15 70.62 - 88.27: 15 Dihedral angle restraints: 1330 sinusoidal: 540 harmonic: 790 Sorted by residual: dihedral pdb=" CA GLN D 38 " pdb=" CB GLN D 38 " pdb=" CG GLN D 38 " pdb=" CD GLN D 38 " ideal model delta sinusoidal sigma weight residual -60.00 -101.30 41.30 3 1.50e+01 4.44e-03 7.38e+00 dihedral pdb=" CA GLN C 38 " pdb=" CB GLN C 38 " pdb=" CG GLN C 38 " pdb=" CD GLN C 38 " ideal model delta sinusoidal sigma weight residual -60.00 -101.25 41.25 3 1.50e+01 4.44e-03 7.37e+00 dihedral pdb=" CA GLN A 38 " pdb=" CB GLN A 38 " pdb=" CG GLN A 38 " pdb=" CD GLN A 38 " ideal model delta sinusoidal sigma weight residual -60.00 -101.23 41.23 3 1.50e+01 4.44e-03 7.37e+00 ... (remaining 1327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 70 0.028 - 0.056: 100 0.056 - 0.084: 45 0.084 - 0.111: 5 0.111 - 0.139: 10 Chirality restraints: 230 Sorted by residual: chirality pdb=" CA GLN E 38 " pdb=" N GLN E 38 " pdb=" C GLN E 38 " pdb=" CB GLN E 38 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA GLN A 38 " pdb=" N GLN A 38 " pdb=" C GLN A 38 " pdb=" CB GLN A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA GLN D 38 " pdb=" N GLN D 38 " pdb=" C GLN D 38 " pdb=" CB GLN D 38 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 227 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 46 " 0.006 2.00e-02 2.50e+03 4.27e-03 3.64e-01 pdb=" CG TYR C 46 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR C 46 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR C 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 46 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 46 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 46 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 46 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 46 " 0.006 2.00e-02 2.50e+03 4.23e-03 3.58e-01 pdb=" CG TYR D 46 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 46 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 46 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 46 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 46 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 46 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 46 " 0.006 2.00e-02 2.50e+03 4.19e-03 3.51e-01 pdb=" CG TYR A 46 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 46 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 46 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 46 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 46 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 46 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 46 " 0.001 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 970 2.93 - 3.42: 1926 3.42 - 3.92: 4408 3.92 - 4.41: 4843 4.41 - 4.90: 8897 Nonbonded interactions: 21044 Sorted by model distance: nonbonded pdb=" NH1 ARG A 28 " pdb=" O GLN B 23 " model vdw 2.441 3.120 nonbonded pdb=" NH1 ARG B 28 " pdb=" O GLN D 23 " model vdw 2.441 3.120 nonbonded pdb=" O GLN C 23 " pdb=" NH1 ARG E 28 " model vdw 2.442 3.120 nonbonded pdb=" O GLN A 23 " pdb=" NH1 ARG C 28 " model vdw 2.444 3.120 nonbonded pdb=" OE1 GLN A 30 " pdb=" NH2 ARG C 28 " model vdw 2.653 3.120 ... (remaining 21039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.740 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2360 Z= 0.304 Angle : 1.158 5.753 3180 Z= 0.701 Chirality : 0.052 0.139 230 Planarity : 0.002 0.012 480 Dihedral : 18.589 88.270 870 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.19), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.15), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 17 TYR 0.010 0.002 TYR C 46 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 2360) covalent geometry : angle 1.15775 ( 3180) hydrogen bonds : bond 0.12709 ( 52) hydrogen bonds : angle 9.27004 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.049 Fit side-chains REVERT: C 60 TYR cc_start: 0.8477 (t80) cc_final: 0.8075 (t80) REVERT: E 24 GLN cc_start: 0.8549 (tm130) cc_final: 0.8220 (tm-30) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.6035 time to fit residues: 18.3755 Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 15 GLN B 8 ASN B 15 GLN B 48 ASN B 61 GLN C 8 ASN C 48 ASN C 61 GLN E 8 ASN E 9 ASN E 15 GLN E 48 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.075516 restraints weight = 2940.843| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.41 r_work: 0.3012 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2360 Z= 0.107 Angle : 0.455 3.334 3180 Z= 0.268 Chirality : 0.035 0.080 230 Planarity : 0.001 0.005 480 Dihedral : 4.202 14.571 340 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (0.22), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.16), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 17 TYR 0.012 0.001 TYR B 46 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 2360) covalent geometry : angle 0.45467 ( 3180) hydrogen bonds : bond 0.02573 ( 52) hydrogen bonds : angle 5.89563 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.085 Fit side-chains REVERT: C 24 GLN cc_start: 0.8352 (tm130) cc_final: 0.7871 (tm-30) REVERT: C 60 TYR cc_start: 0.8454 (t80) cc_final: 0.8099 (t80) REVERT: E 24 GLN cc_start: 0.8529 (tm130) cc_final: 0.7716 (tm130) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.6587 time to fit residues: 16.0835 Evaluate side-chains 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN C 8 ASN C 61 GLN D 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.082772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.071355 restraints weight = 3018.992| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.41 r_work: 0.2933 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2360 Z= 0.284 Angle : 0.565 3.849 3180 Z= 0.336 Chirality : 0.037 0.085 230 Planarity : 0.003 0.017 480 Dihedral : 4.601 16.567 340 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 17 TYR 0.016 0.002 TYR A 46 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 2360) covalent geometry : angle 0.56502 ( 3180) hydrogen bonds : bond 0.03567 ( 52) hydrogen bonds : angle 5.96735 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.054 Fit side-chains REVERT: C 24 GLN cc_start: 0.8488 (tm130) cc_final: 0.7989 (tm-30) REVERT: E 24 GLN cc_start: 0.8494 (tm130) cc_final: 0.7721 (tm130) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.6114 time to fit residues: 14.3094 Evaluate side-chains 24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.086020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.074652 restraints weight = 2985.443| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.42 r_work: 0.3001 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2360 Z= 0.097 Angle : 0.447 3.378 3180 Z= 0.262 Chirality : 0.035 0.067 230 Planarity : 0.001 0.006 480 Dihedral : 4.073 14.185 340 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 17 TYR 0.011 0.001 TYR D 60 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 2360) covalent geometry : angle 0.44725 ( 3180) hydrogen bonds : bond 0.02209 ( 52) hydrogen bonds : angle 5.25502 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.052 Fit side-chains REVERT: C 24 GLN cc_start: 0.8402 (tm130) cc_final: 0.7951 (tm-30) REVERT: E 24 GLN cc_start: 0.8474 (tm130) cc_final: 0.7708 (tm130) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.5794 time to fit residues: 12.9681 Evaluate side-chains 21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN C 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.074271 restraints weight = 2946.509| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.41 r_work: 0.2997 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2360 Z= 0.118 Angle : 0.460 3.453 3180 Z= 0.270 Chirality : 0.035 0.067 230 Planarity : 0.002 0.008 480 Dihedral : 4.065 14.800 340 Min Nonbonded Distance : 2.681 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.48 % Allowed : 3.33 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 17 TYR 0.012 0.002 TYR D 60 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2360) covalent geometry : angle 0.45960 ( 3180) hydrogen bonds : bond 0.02292 ( 52) hydrogen bonds : angle 5.16406 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.086 Fit side-chains REVERT: C 24 GLN cc_start: 0.8387 (tm130) cc_final: 0.7925 (tm-30) REVERT: E 24 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7732 (tm130) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.6616 time to fit residues: 15.5023 Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN B 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072624 restraints weight = 2953.577| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.40 r_work: 0.2958 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2360 Z= 0.196 Angle : 0.512 3.667 3180 Z= 0.302 Chirality : 0.036 0.078 230 Planarity : 0.002 0.014 480 Dihedral : 4.287 15.383 340 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.48 % Allowed : 3.33 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 17 TYR 0.014 0.002 TYR A 46 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 2360) covalent geometry : angle 0.51158 ( 3180) hydrogen bonds : bond 0.02893 ( 52) hydrogen bonds : angle 5.44815 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.058 Fit side-chains REVERT: C 24 GLN cc_start: 0.8425 (tm130) cc_final: 0.7956 (tm-30) REVERT: E 24 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7677 (tm130) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.6107 time to fit residues: 12.4206 Evaluate side-chains 21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.084912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.073511 restraints weight = 2977.017| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.42 r_work: 0.2981 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2360 Z= 0.125 Angle : 0.469 3.501 3180 Z= 0.275 Chirality : 0.035 0.068 230 Planarity : 0.002 0.009 480 Dihedral : 4.088 14.924 340 Min Nonbonded Distance : 2.687 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.48 % Allowed : 3.33 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 17 TYR 0.013 0.002 TYR C 13 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2360) covalent geometry : angle 0.46867 ( 3180) hydrogen bonds : bond 0.02391 ( 52) hydrogen bonds : angle 5.20439 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.053 Fit side-chains REVERT: C 24 GLN cc_start: 0.8377 (tm130) cc_final: 0.7908 (tm-30) REVERT: E 24 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7681 (tm130) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.6443 time to fit residues: 13.7481 Evaluate side-chains 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.085978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.074800 restraints weight = 2927.559| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.39 r_work: 0.2980 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2360 Z= 0.139 Angle : 0.481 3.544 3180 Z= 0.282 Chirality : 0.035 0.072 230 Planarity : 0.002 0.010 480 Dihedral : 4.122 14.946 340 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.48 % Allowed : 3.81 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 17 TYR 0.014 0.002 TYR C 13 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 2360) covalent geometry : angle 0.48063 ( 3180) hydrogen bonds : bond 0.02476 ( 52) hydrogen bonds : angle 5.23015 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.052 Fit side-chains REVERT: C 24 GLN cc_start: 0.8383 (tm130) cc_final: 0.7918 (tm-30) REVERT: E 24 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7691 (tm130) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.6143 time to fit residues: 13.1125 Evaluate side-chains 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.085796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.074413 restraints weight = 2999.052| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.42 r_work: 0.3001 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2360 Z= 0.109 Angle : 0.459 3.446 3180 Z= 0.268 Chirality : 0.035 0.067 230 Planarity : 0.001 0.008 480 Dihedral : 3.995 14.441 340 Min Nonbonded Distance : 2.689 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.48 % Allowed : 3.33 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 17 TYR 0.016 0.002 TYR C 13 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 2360) covalent geometry : angle 0.45906 ( 3180) hydrogen bonds : bond 0.02241 ( 52) hydrogen bonds : angle 5.09623 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.086 Fit side-chains REVERT: C 24 GLN cc_start: 0.8372 (tm130) cc_final: 0.7903 (tm-30) REVERT: E 24 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7696 (tm130) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.6345 time to fit residues: 14.2211 Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.073552 restraints weight = 3014.974| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.41 r_work: 0.2963 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2360 Z= 0.176 Angle : 0.502 3.620 3180 Z= 0.296 Chirality : 0.036 0.076 230 Planarity : 0.002 0.011 480 Dihedral : 4.201 15.242 340 Min Nonbonded Distance : 2.683 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.48 % Allowed : 3.33 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 17 TYR 0.017 0.002 TYR C 60 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 2360) covalent geometry : angle 0.50228 ( 3180) hydrogen bonds : bond 0.02757 ( 52) hydrogen bonds : angle 5.31655 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.052 Fit side-chains REVERT: C 24 GLN cc_start: 0.8373 (tm130) cc_final: 0.7891 (tm-30) REVERT: E 24 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7692 (tm130) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.5981 time to fit residues: 13.3875 Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 17 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.075077 restraints weight = 3010.031| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.43 r_work: 0.3022 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2360 Z= 0.087 Angle : 0.443 3.341 3180 Z= 0.258 Chirality : 0.035 0.068 230 Planarity : 0.001 0.007 480 Dihedral : 3.894 13.932 340 Min Nonbonded Distance : 2.692 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.48 % Allowed : 3.33 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 17 TYR 0.017 0.001 TYR C 13 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 2360) covalent geometry : angle 0.44269 ( 3180) hydrogen bonds : bond 0.02040 ( 52) hydrogen bonds : angle 4.96817 ( 156) =============================================================================== Job complete usr+sys time: 758.61 seconds wall clock time: 13 minutes 53.83 seconds (833.83 seconds total)