Starting phenix.real_space_refine on Wed Sep 17 05:12:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywx_39646/09_2025/8ywx_39646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywx_39646/09_2025/8ywx_39646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ywx_39646/09_2025/8ywx_39646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywx_39646/09_2025/8ywx_39646.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywx_39646/09_2025/8ywx_39646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywx_39646/09_2025/8ywx_39646.cif" } resolution = 3.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= -0.001 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3035 2.51 5 N 817 2.21 5 O 932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4803 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1618 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain: "D" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1645 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "A" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1540 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Time building chain proxies: 1.28, per 1000 atoms: 0.27 Number of scatterers: 4803 At special positions: 0 Unit cell: (60.872, 79.351, 123.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 932 8.00 N 817 7.00 C 3035 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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: 0.31 Conformation dependent library (CDL) restraints added in 179.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1148 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 15 sheets defined 9.8% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.581A pdb=" N ASN E 32 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.580A pdb=" N LYS E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.163A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.872A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.235A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.543A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 18 through 21 removed outlier: 3.628A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.173A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR E 94 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER E 106 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.173A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR E 94 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 124 through 127 removed outlier: 5.226A pdb=" N ALA E 141 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL E 188 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY E 143 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL E 186 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER E 184 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS E 147 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU E 182 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 124 through 127 removed outlier: 5.226A pdb=" N ALA E 141 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL E 188 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY E 143 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL E 186 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU E 145 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER E 184 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS E 147 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU E 182 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER E 181 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 173 " --> pdb=" O SER E 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 154 through 158 removed outlier: 3.554A pdb=" N THR E 155 " --> pdb=" O ASN E 203 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR E 198 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL E 211 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.694A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.743A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LYS D 107 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA D 13 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D 86 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.927A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS D 134 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 176 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN D 160 " --> pdb=" O THR D 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 145 through 147 removed outlier: 4.210A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 197 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN D 147 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU D 195 " --> pdb=" O GLN D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 149 through 150 Processing sheet with id=AB3, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.033A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 474 135 hydrogen bonds defined for protein. 324 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: 0.69 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 783 1.26 - 1.40: 1269 1.40 - 1.54: 2811 1.54 - 1.68: 35 1.68 - 1.82: 22 Bond restraints: 4920 Sorted by residual: bond pdb=" C GLY E 103 " pdb=" N GLY E 104 " ideal model delta sigma weight residual 1.333 1.125 0.208 2.26e-02 1.96e+03 8.50e+01 bond pdb=" C VAL E 2 " pdb=" N GLN E 3 " ideal model delta sigma weight residual 1.331 1.199 0.132 1.55e-02 4.16e+03 7.24e+01 bond pdb=" CA SER A 438 " pdb=" CB SER A 438 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.21e-02 6.83e+03 4.04e+01 bond pdb=" CA SER A 349 " pdb=" CB SER A 349 " ideal model delta sigma weight residual 1.528 1.439 0.089 1.61e-02 3.86e+03 3.08e+01 bond pdb=" N PRO D 59 " pdb=" CD PRO D 59 " ideal model delta sigma weight residual 1.473 1.543 -0.070 1.40e-02 5.10e+03 2.51e+01 ... (remaining 4915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.87: 6514 6.87 - 13.75: 127 13.75 - 20.62: 28 20.62 - 27.50: 14 27.50 - 34.37: 6 Bond angle restraints: 6689 Sorted by residual: angle pdb=" C ALA E 24 " pdb=" CA ALA E 24 " pdb=" CB ALA E 24 " ideal model delta sigma weight residual 110.62 77.60 33.02 1.46e+00 4.69e-01 5.11e+02 angle pdb=" N LEU E 11 " pdb=" CA LEU E 11 " pdb=" C LEU E 11 " ideal model delta sigma weight residual 110.17 144.54 -34.37 1.61e+00 3.86e-01 4.56e+02 angle pdb=" N ASP E 10 " pdb=" CA ASP E 10 " pdb=" C ASP E 10 " ideal model delta sigma weight residual 107.73 80.07 27.66 1.34e+00 5.57e-01 4.26e+02 angle pdb=" C LEU E 11 " pdb=" CA LEU E 11 " pdb=" CB LEU E 11 " ideal model delta sigma weight residual 109.50 80.28 29.22 1.69e+00 3.50e-01 2.99e+02 angle pdb=" N LEU E 11 " pdb=" CA LEU E 11 " pdb=" CB LEU E 11 " ideal model delta sigma weight residual 110.63 82.76 27.87 1.63e+00 3.76e-01 2.92e+02 ... (remaining 6684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2661 17.76 - 35.51: 224 35.51 - 53.27: 34 53.27 - 71.03: 14 71.03 - 88.78: 5 Dihedral angle restraints: 2938 sinusoidal: 1136 harmonic: 1802 Sorted by residual: dihedral pdb=" C LEU E 11 " pdb=" N LEU E 11 " pdb=" CA LEU E 11 " pdb=" CB LEU E 11 " ideal model delta harmonic sigma weight residual -122.60 -61.86 -60.74 0 2.50e+00 1.60e-01 5.90e+02 dihedral pdb=" N LEU E 11 " pdb=" C LEU E 11 " pdb=" CA LEU E 11 " pdb=" CB LEU E 11 " ideal model delta harmonic sigma weight residual 122.80 62.56 60.24 0 2.50e+00 1.60e-01 5.81e+02 dihedral pdb=" C ALA E 24 " pdb=" N ALA E 24 " pdb=" CA ALA E 24 " pdb=" CB ALA E 24 " ideal model delta harmonic sigma weight residual -122.60 -89.41 -33.19 0 2.50e+00 1.60e-01 1.76e+02 ... (remaining 2935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 646 0.175 - 0.350: 64 0.350 - 0.525: 17 0.525 - 0.700: 3 0.700 - 0.875: 4 Chirality restraints: 734 Sorted by residual: chirality pdb=" CA PHE A 338 " pdb=" N PHE A 338 " pdb=" C PHE A 338 " pdb=" CB PHE A 338 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" CA SER E 30 " pdb=" N SER E 30 " pdb=" C SER E 30 " pdb=" CB SER E 30 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.90e+01 chirality pdb=" CA LEU E 11 " pdb=" N LEU E 11 " pdb=" C LEU E 11 " pdb=" CB LEU E 11 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 731 not shown) Planarity restraints: 868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 58 " -0.103 5.00e-02 4.00e+02 1.54e-01 3.80e+01 pdb=" N PRO D 59 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " -0.088 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 5 " 0.030 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C VAL E 5 " -0.104 2.00e-02 2.50e+03 pdb=" O VAL E 5 " 0.040 2.00e-02 2.50e+03 pdb=" N GLU E 6 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 2 " -0.026 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C VAL E 2 " 0.084 2.00e-02 2.50e+03 pdb=" O VAL E 2 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN E 3 " -0.030 2.00e-02 2.50e+03 ... (remaining 865 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 71 2.50 - 3.10: 3410 3.10 - 3.70: 6950 3.70 - 4.30: 10010 4.30 - 4.90: 16430 Nonbonded interactions: 36871 Sorted by model distance: nonbonded pdb=" O GLY E 104 " pdb=" OD1 ASP E 105 " model vdw 1.898 3.040 nonbonded pdb=" N ASP E 10 " pdb=" O ASP E 10 " model vdw 1.898 2.496 nonbonded pdb=" O SER A 349 " pdb=" O ALA A 352 " model vdw 1.953 3.040 nonbonded pdb=" O LYS D 31 " pdb=" O ASP D 50 " model vdw 1.984 3.040 nonbonded pdb=" O ALA E 24 " pdb=" CB ALA E 24 " model vdw 2.007 2.768 ... (remaining 36866 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.250 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.009 0.208 4928 Z= 0.621 Angle : 2.558 34.370 6705 Z= 1.695 Chirality : 0.134 0.875 734 Planarity : 0.010 0.154 868 Dihedral : 13.583 88.783 1766 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.43 % Allowed : 3.18 % Favored : 94.38 % Cbeta Deviations : 8.01 % Peptide Plane: Cis-proline : 8.82 % 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 aren not related in a simple way. whole: -1.55 (0.33), residues: 617 helix: -2.77 (0.70), residues: 35 sheet: -0.44 (0.38), residues: 168 loop : -1.15 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 355 TYR 0.029 0.002 TYR A 453 PHE 0.020 0.002 PHE A 400 TRP 0.044 0.003 TRP A 353 HIS 0.006 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00907 ( 4920) covalent geometry : angle 2.55852 ( 6689) SS BOND : bond 0.01118 ( 8) SS BOND : angle 2.22206 ( 16) hydrogen bonds : bond 0.30321 ( 107) hydrogen bonds : angle 11.68204 ( 324) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 TYR cc_start: 0.6149 (m-80) cc_final: 0.5763 (m-80) REVERT: E 210 LYS cc_start: 0.8413 (mmpt) cc_final: 0.8035 (mmmt) REVERT: A 453 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7555 (p90) outliers start: 13 outliers final: 6 residues processed: 88 average time/residue: 0.0998 time to fit residues: 10.6343 Evaluate side-chains 54 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 488 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 0.0060 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN D 27 GLN D 155 GLN A 360 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.129487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.105200 restraints weight = 13850.992| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 3.94 r_work: 0.3699 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4928 Z= 0.162 Angle : 0.681 7.810 6705 Z= 0.365 Chirality : 0.048 0.243 734 Planarity : 0.006 0.062 868 Dihedral : 6.521 49.260 694 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.18 % Allowed : 9.74 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -1.53 (0.33), residues: 617 helix: -2.29 (0.81), residues: 27 sheet: -0.37 (0.37), residues: 183 loop : -1.27 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 31 TYR 0.019 0.002 TYR D 140 PHE 0.023 0.002 PHE A 377 TRP 0.019 0.002 TRP A 353 HIS 0.003 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4920) covalent geometry : angle 0.67244 ( 6689) SS BOND : bond 0.01033 ( 8) SS BOND : angle 2.26115 ( 16) hydrogen bonds : bond 0.04075 ( 107) hydrogen bonds : angle 6.40501 ( 324) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.217 Fit side-chains REVERT: E 98 ASP cc_start: 0.7685 (t0) cc_final: 0.7462 (t0) REVERT: E 203 ASN cc_start: 0.7406 (m-40) cc_final: 0.6970 (m110) REVERT: E 205 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8742 (ptpt) REVERT: E 210 LYS cc_start: 0.8682 (mmpt) cc_final: 0.8004 (mmmt) REVERT: D 105 GLU cc_start: 0.7940 (pm20) cc_final: 0.7385 (pm20) outliers start: 17 outliers final: 10 residues processed: 72 average time/residue: 0.0894 time to fit residues: 8.1265 Evaluate side-chains 56 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.127861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.103453 restraints weight = 13340.431| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.84 r_work: 0.3647 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4928 Z= 0.142 Angle : 0.661 12.297 6705 Z= 0.350 Chirality : 0.047 0.285 734 Planarity : 0.006 0.051 868 Dihedral : 5.453 45.221 683 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.12 % Allowed : 10.11 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -1.41 (0.33), residues: 617 helix: -1.82 (1.15), residues: 14 sheet: -0.25 (0.39), residues: 173 loop : -1.27 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 19 TYR 0.014 0.002 TYR A 369 PHE 0.018 0.001 PHE A 377 TRP 0.012 0.002 TRP A 353 HIS 0.002 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4920) covalent geometry : angle 0.64175 ( 6689) SS BOND : bond 0.01311 ( 8) SS BOND : angle 3.34642 ( 16) hydrogen bonds : bond 0.04017 ( 107) hydrogen bonds : angle 5.80358 ( 324) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: E 203 ASN cc_start: 0.7508 (m-40) cc_final: 0.7156 (m110) REVERT: E 210 LYS cc_start: 0.8617 (mmpt) cc_final: 0.8266 (mmmt) REVERT: D 183 LYS cc_start: 0.0791 (pttm) cc_final: -0.0066 (ptmt) REVERT: A 389 ASP cc_start: 0.8686 (m-30) cc_final: 0.8359 (p0) outliers start: 22 outliers final: 12 residues processed: 75 average time/residue: 0.1020 time to fit residues: 9.3285 Evaluate side-chains 54 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.0070 chunk 32 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 0.0570 chunk 39 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.130237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.107774 restraints weight = 13551.208| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 3.74 r_work: 0.3771 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4928 Z= 0.113 Angle : 0.691 19.117 6705 Z= 0.357 Chirality : 0.048 0.363 734 Planarity : 0.005 0.044 868 Dihedral : 5.157 48.556 683 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.00 % Allowed : 12.55 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -1.32 (0.33), residues: 617 helix: -2.03 (1.12), residues: 16 sheet: -0.09 (0.38), residues: 172 loop : -1.23 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 3 TYR 0.017 0.001 TYR A 423 PHE 0.011 0.001 PHE A 456 TRP 0.013 0.001 TRP A 436 HIS 0.002 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4920) covalent geometry : angle 0.66484 ( 6689) SS BOND : bond 0.00880 ( 8) SS BOND : angle 3.89312 ( 16) hydrogen bonds : bond 0.03941 ( 107) hydrogen bonds : angle 5.18567 ( 324) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: E 203 ASN cc_start: 0.7788 (m-40) cc_final: 0.7513 (m-40) REVERT: E 205 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8620 (mttp) REVERT: E 210 LYS cc_start: 0.8571 (mmpt) cc_final: 0.7834 (mmmm) REVERT: D 126 LYS cc_start: 0.2821 (tptm) cc_final: 0.2272 (tmtt) REVERT: D 183 LYS cc_start: 0.1507 (pttm) cc_final: 0.0557 (pttm) REVERT: A 465 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6842 (tm-30) outliers start: 16 outliers final: 9 residues processed: 66 average time/residue: 0.1059 time to fit residues: 8.5021 Evaluate side-chains 53 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.128660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.104724 restraints weight = 13881.669| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.80 r_work: 0.3724 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4928 Z= 0.118 Angle : 0.656 14.927 6705 Z= 0.341 Chirality : 0.047 0.311 734 Planarity : 0.005 0.040 868 Dihedral : 5.003 44.665 683 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.43 % Allowed : 12.73 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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 aren not related in a simple way. whole: -1.38 (0.33), residues: 617 helix: -2.52 (0.82), residues: 24 sheet: -0.02 (0.39), residues: 171 loop : -1.26 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 355 TYR 0.014 0.001 TYR A 369 PHE 0.011 0.001 PHE D 73 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4920) covalent geometry : angle 0.62964 ( 6689) SS BOND : bond 0.00621 ( 8) SS BOND : angle 3.81680 ( 16) hydrogen bonds : bond 0.03804 ( 107) hydrogen bonds : angle 5.14487 ( 324) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: E 89 ASP cc_start: 0.7817 (t70) cc_final: 0.7459 (t0) REVERT: E 214 LYS cc_start: 0.6566 (tptt) cc_final: 0.6150 (tptt) REVERT: D 126 LYS cc_start: 0.2770 (tptm) cc_final: 0.2346 (tmtt) REVERT: D 183 LYS cc_start: 0.1710 (pttm) cc_final: -0.0426 (pttt) REVERT: A 378 LYS cc_start: 0.8570 (tttp) cc_final: 0.8294 (tttp) REVERT: A 465 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6744 (tm-30) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.1172 time to fit residues: 8.8230 Evaluate side-chains 53 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.127762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.103845 restraints weight = 13882.087| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 3.76 r_work: 0.3720 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4928 Z= 0.136 Angle : 0.662 12.265 6705 Z= 0.345 Chirality : 0.046 0.262 734 Planarity : 0.005 0.038 868 Dihedral : 4.673 31.788 681 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.37 % Allowed : 12.55 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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 aren not related in a simple way. whole: -1.33 (0.33), residues: 617 helix: -2.41 (0.82), residues: 22 sheet: -0.23 (0.37), residues: 180 loop : -1.14 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 18 TYR 0.014 0.002 TYR A 369 PHE 0.013 0.001 PHE D 73 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4920) covalent geometry : angle 0.64112 ( 6689) SS BOND : bond 0.00513 ( 8) SS BOND : angle 3.45808 ( 16) hydrogen bonds : bond 0.03768 ( 107) hydrogen bonds : angle 5.21512 ( 324) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.198 Fit side-chains REVERT: E 205 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8590 (mttp) REVERT: D 126 LYS cc_start: 0.2768 (tptm) cc_final: 0.2445 (tmtt) REVERT: D 183 LYS cc_start: 0.1711 (pttm) cc_final: -0.0399 (pttt) REVERT: A 465 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6787 (tm-30) outliers start: 18 outliers final: 13 residues processed: 64 average time/residue: 0.0972 time to fit residues: 7.7151 Evaluate side-chains 53 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 11 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.125803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.100429 restraints weight = 13526.531| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.27 r_work: 0.3694 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4928 Z= 0.194 Angle : 0.758 18.103 6705 Z= 0.393 Chirality : 0.048 0.306 734 Planarity : 0.005 0.036 868 Dihedral : 5.248 42.175 681 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.00 % Allowed : 13.48 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -1.50 (0.33), residues: 617 helix: -3.47 (0.53), residues: 29 sheet: -0.37 (0.37), residues: 180 loop : -1.12 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 18 TYR 0.019 0.002 TYR A 423 PHE 0.018 0.002 PHE D 73 TRP 0.010 0.002 TRP A 436 HIS 0.004 0.001 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 4920) covalent geometry : angle 0.73439 ( 6689) SS BOND : bond 0.00681 ( 8) SS BOND : angle 3.91612 ( 16) hydrogen bonds : bond 0.04053 ( 107) hydrogen bonds : angle 5.65905 ( 324) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.193 Fit side-chains REVERT: D 183 LYS cc_start: 0.2608 (pttm) cc_final: 0.0397 (pttm) outliers start: 16 outliers final: 16 residues processed: 60 average time/residue: 0.1025 time to fit residues: 7.5749 Evaluate side-chains 56 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.129246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.104147 restraints weight = 14083.186| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.50 r_work: 0.3746 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4928 Z= 0.122 Angle : 0.686 16.221 6705 Z= 0.353 Chirality : 0.047 0.266 734 Planarity : 0.005 0.035 868 Dihedral : 4.731 29.868 681 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.81 % Allowed : 14.98 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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 aren not related in a simple way. whole: -1.31 (0.34), residues: 617 helix: -2.85 (0.72), residues: 24 sheet: -0.26 (0.37), residues: 182 loop : -1.06 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 18 TYR 0.024 0.001 TYR A 423 PHE 0.011 0.001 PHE D 73 TRP 0.013 0.001 TRP A 436 HIS 0.003 0.001 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4920) covalent geometry : angle 0.66347 ( 6689) SS BOND : bond 0.00461 ( 8) SS BOND : angle 3.63708 ( 16) hydrogen bonds : bond 0.03546 ( 107) hydrogen bonds : angle 5.13638 ( 324) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: E 89 ASP cc_start: 0.7463 (t70) cc_final: 0.7188 (t0) REVERT: D 183 LYS cc_start: 0.2373 (pttm) cc_final: 0.0238 (pttm) outliers start: 15 outliers final: 13 residues processed: 63 average time/residue: 0.1151 time to fit residues: 8.7290 Evaluate side-chains 54 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.127318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.104374 restraints weight = 13844.937| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 3.86 r_work: 0.3694 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4928 Z= 0.167 Angle : 0.743 16.376 6705 Z= 0.384 Chirality : 0.048 0.264 734 Planarity : 0.005 0.035 868 Dihedral : 4.973 36.181 681 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.37 % Allowed : 14.61 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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 aren not related in a simple way. whole: -1.36 (0.34), residues: 617 helix: -2.66 (0.81), residues: 22 sheet: -0.36 (0.37), residues: 183 loop : -1.08 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 3 TYR 0.023 0.002 TYR A 423 PHE 0.014 0.001 PHE D 73 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 4920) covalent geometry : angle 0.72085 ( 6689) SS BOND : bond 0.00589 ( 8) SS BOND : angle 3.73667 ( 16) hydrogen bonds : bond 0.03976 ( 107) hydrogen bonds : angle 5.49042 ( 324) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.198 Fit side-chains REVERT: D 126 LYS cc_start: 0.1630 (ttpp) cc_final: 0.0534 (ttpp) REVERT: D 183 LYS cc_start: 0.2615 (pttm) cc_final: 0.0562 (pttm) outliers start: 18 outliers final: 15 residues processed: 64 average time/residue: 0.0992 time to fit residues: 7.8809 Evaluate side-chains 59 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.126405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.103147 restraints weight = 13826.723| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.87 r_work: 0.3676 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4928 Z= 0.190 Angle : 0.793 16.148 6705 Z= 0.409 Chirality : 0.049 0.321 734 Planarity : 0.005 0.035 868 Dihedral : 5.326 39.649 681 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.18 % Allowed : 14.79 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -1.49 (0.34), residues: 617 helix: -2.89 (0.78), residues: 22 sheet: -0.53 (0.37), residues: 184 loop : -1.12 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 3 TYR 0.023 0.002 TYR A 423 PHE 0.016 0.002 PHE D 73 TRP 0.012 0.002 TRP E 158 HIS 0.004 0.001 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 4920) covalent geometry : angle 0.76882 ( 6689) SS BOND : bond 0.00716 ( 8) SS BOND : angle 4.03047 ( 16) hydrogen bonds : bond 0.04220 ( 107) hydrogen bonds : angle 5.79440 ( 324) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.164 Fit side-chains REVERT: E 210 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8182 (mmmt) REVERT: D 126 LYS cc_start: 0.1335 (ttpp) cc_final: 0.0060 (ttpp) REVERT: D 183 LYS cc_start: 0.2817 (pttm) cc_final: 0.0735 (pttm) outliers start: 17 outliers final: 16 residues processed: 61 average time/residue: 0.0974 time to fit residues: 7.4290 Evaluate side-chains 60 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 101 ARG Chi-restraints excluded: chain E residue 144 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.127835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.104013 restraints weight = 13926.362| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.80 r_work: 0.3692 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4928 Z= 0.150 Angle : 0.745 14.936 6705 Z= 0.384 Chirality : 0.048 0.302 734 Planarity : 0.005 0.047 868 Dihedral : 4.962 33.445 681 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.18 % Allowed : 14.61 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -1.46 (0.34), residues: 617 helix: -2.63 (0.84), residues: 22 sheet: -0.50 (0.37), residues: 183 loop : -1.12 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 3 TYR 0.023 0.002 TYR A 423 PHE 0.012 0.001 PHE A 374 TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS D 198 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4920) covalent geometry : angle 0.72175 ( 6689) SS BOND : bond 0.00537 ( 8) SS BOND : angle 3.85661 ( 16) hydrogen bonds : bond 0.03912 ( 107) hydrogen bonds : angle 5.51872 ( 324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1570.34 seconds wall clock time: 27 minutes 44.04 seconds (1664.04 seconds total)