Starting phenix.real_space_refine on Sun Apr 27 06:52:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywx_39646/04_2025/8ywx_39646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywx_39646/04_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_39646/04_2025/8ywx_39646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywx_39646/04_2025/8ywx_39646.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywx_39646/04_2025/8ywx_39646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywx_39646/04_2025/8ywx_39646.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.74, per 1000 atoms: 0.99 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: 1.20 Conformation dependent library (CDL) restraints added in 920.8 milliseconds 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: 0.79 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: 1.44 Time building geometry restraints manager: 1.43 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: 6.800 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.460 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (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 TRP 0.044 0.003 TRP A 353 HIS 0.006 0.001 HIS E 102 PHE 0.020 0.002 PHE A 400 TYR 0.029 0.002 TYR A 453 ARG 0.003 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.30321 ( 107) hydrogen bonds : angle 11.68204 ( 324) SS BOND : bond 0.01118 ( 8) SS BOND : angle 2.22206 ( 16) covalent geometry : bond 0.00907 ( 4920) covalent geometry : angle 2.55852 ( 6689) *********************** 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 : 0.574 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: 0.2212 time to fit residues: 23.7866 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 : 0.555 ------------------------------------------------------------------------------- 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 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.0030 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.130561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.104197 restraints weight = 13692.136| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 3.38 r_work: 0.3753 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2547 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= 0.140 Angle : 0.660 7.932 6705 Z= 0.354 Chirality : 0.048 0.218 734 Planarity : 0.006 0.062 868 Dihedral : 6.491 53.053 694 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.81 % Allowed : 9.93 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.33), residues: 617 helix: -1.95 (0.93), residues: 21 sheet: -0.37 (0.37), residues: 184 loop : -1.22 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 353 HIS 0.003 0.001 HIS E 102 PHE 0.025 0.002 PHE A 377 TYR 0.017 0.002 TYR D 140 ARG 0.003 0.000 ARG E 71 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 107) hydrogen bonds : angle 6.36411 ( 324) SS BOND : bond 0.00655 ( 8) SS BOND : angle 2.21191 ( 16) covalent geometry : bond 0.00316 ( 4920) covalent geometry : angle 0.65216 ( 6689) *********************** 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: 15 poor density : 62 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: E 3 GLN cc_start: 0.7912 (pp30) cc_final: 0.7686 (pp30) REVERT: E 203 ASN cc_start: 0.7408 (m-40) cc_final: 0.7009 (m110) REVERT: E 210 LYS cc_start: 0.8689 (mmpt) cc_final: 0.8264 (mmmt) outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 0.2093 time to fit residues: 19.6246 Evaluate side-chains 51 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 SER 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 433 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 A 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.125914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.099369 restraints weight = 13209.990| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.98 r_work: 0.3579 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4928 Z= 0.205 Angle : 0.711 11.143 6705 Z= 0.380 Chirality : 0.048 0.304 734 Planarity : 0.006 0.054 868 Dihedral : 5.796 42.391 683 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.31 % Allowed : 10.30 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.33), residues: 617 helix: -2.38 (0.93), residues: 20 sheet: -0.37 (0.38), residues: 176 loop : -1.29 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.003 0.001 HIS E 102 PHE 0.018 0.002 PHE A 377 TYR 0.017 0.002 TYR A 369 ARG 0.004 0.001 ARG E 31 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 107) hydrogen bonds : angle 6.17884 ( 324) SS BOND : bond 0.01159 ( 8) SS BOND : angle 3.31084 ( 16) covalent geometry : bond 0.00463 ( 4920) covalent geometry : angle 0.69306 ( 6689) *********************** 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 83 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 TYR cc_start: 0.8199 (m-10) cc_final: 0.7932 (m-10) REVERT: E 203 ASN cc_start: 0.7605 (m-40) cc_final: 0.7294 (m110) REVERT: E 210 LYS cc_start: 0.8679 (mmpt) cc_final: 0.8349 (mmmm) REVERT: D 183 LYS cc_start: 0.1578 (pttm) cc_final: -0.0487 (pttt) REVERT: A 389 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8496 (p0) REVERT: A 465 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7328 (tm-30) outliers start: 23 outliers final: 11 residues processed: 76 average time/residue: 0.2519 time to fit residues: 24.0240 Evaluate side-chains 58 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 135 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 406 GLU 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 21 optimal weight: 0.0370 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.127886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.102147 restraints weight = 13890.310| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.28 r_work: 0.3720 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4928 Z= 0.126 Angle : 0.727 20.687 6705 Z= 0.372 Chirality : 0.047 0.352 734 Planarity : 0.005 0.045 868 Dihedral : 5.386 48.160 683 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.25 % Allowed : 13.11 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.33), residues: 617 helix: -1.94 (1.22), residues: 14 sheet: -0.31 (0.38), residues: 177 loop : -1.25 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.002 0.001 HIS E 102 PHE 0.018 0.001 PHE A 377 TYR 0.018 0.002 TYR A 423 ARG 0.003 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 107) hydrogen bonds : angle 5.48081 ( 324) SS BOND : bond 0.00857 ( 8) SS BOND : angle 4.28243 ( 16) covalent geometry : bond 0.00283 ( 4920) covalent geometry : angle 0.69702 ( 6689) *********************** 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 64 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: E 59 TYR cc_start: 0.7935 (m-10) cc_final: 0.7697 (m-10) REVERT: E 205 LYS cc_start: 0.9019 (mmmt) cc_final: 0.8601 (ptpp) REVERT: E 210 LYS cc_start: 0.8630 (mmpt) cc_final: 0.7924 (mmmm) REVERT: D 126 LYS cc_start: 0.2783 (tptm) cc_final: 0.2471 (tmtt) REVERT: D 183 LYS cc_start: 0.1866 (pttm) cc_final: -0.0325 (pttt) REVERT: A 389 ASP cc_start: 0.8435 (m-30) cc_final: 0.8139 (p0) REVERT: A 465 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6843 (tm-30) REVERT: A 471 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7263 (pm20) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 0.2233 time to fit residues: 17.3299 Evaluate side-chains 54 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL 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 Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 0.0270 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 0.0000 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.127421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.103042 restraints weight = 13964.021| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.65 r_work: 0.3697 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4928 Z= 0.134 Angle : 0.697 22.215 6705 Z= 0.358 Chirality : 0.047 0.300 734 Planarity : 0.005 0.041 868 Dihedral : 5.222 43.936 683 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.18 % Allowed : 11.99 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.33), residues: 617 helix: -1.97 (1.19), residues: 14 sheet: -0.33 (0.37), residues: 182 loop : -1.22 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS E 102 PHE 0.012 0.001 PHE D 73 TYR 0.014 0.001 TYR A 423 ARG 0.002 0.000 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 107) hydrogen bonds : angle 5.46609 ( 324) SS BOND : bond 0.00851 ( 8) SS BOND : angle 3.97285 ( 16) covalent geometry : bond 0.00301 ( 4920) covalent geometry : angle 0.67010 ( 6689) *********************** 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 72 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 TYR cc_start: 0.7979 (m-10) cc_final: 0.7751 (m-10) REVERT: E 210 LYS cc_start: 0.8488 (mmpt) cc_final: 0.8051 (mmmm) REVERT: D 126 LYS cc_start: 0.2630 (tptm) cc_final: 0.2296 (tmtt) REVERT: D 183 LYS cc_start: 0.1614 (pttm) cc_final: -0.0372 (pttm) REVERT: A 465 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6813 (tm-30) outliers start: 17 outliers final: 11 residues processed: 69 average time/residue: 0.2330 time to fit residues: 19.8721 Evaluate side-chains 54 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL 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 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 Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.125244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.099585 restraints weight = 13784.351| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.28 r_work: 0.3671 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4928 Z= 0.207 Angle : 0.803 21.400 6705 Z= 0.412 Chirality : 0.049 0.353 734 Planarity : 0.005 0.040 868 Dihedral : 5.792 41.269 683 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.93 % Allowed : 11.99 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.33), residues: 617 helix: -3.45 (0.63), residues: 21 sheet: -0.48 (0.36), residues: 181 loop : -1.10 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 353 HIS 0.004 0.001 HIS D 198 PHE 0.021 0.002 PHE D 73 TYR 0.018 0.002 TYR A 369 ARG 0.003 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 107) hydrogen bonds : angle 5.95167 ( 324) SS BOND : bond 0.00802 ( 8) SS BOND : angle 4.44608 ( 16) covalent geometry : bond 0.00471 ( 4920) covalent geometry : angle 0.77378 ( 6689) *********************** 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 69 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: E 205 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8568 (mttp) REVERT: E 210 LYS cc_start: 0.8324 (mmpt) cc_final: 0.7581 (mmmm) REVERT: D 183 LYS cc_start: 0.2664 (pttm) cc_final: 0.0652 (pttm) outliers start: 21 outliers final: 18 residues processed: 68 average time/residue: 0.2351 time to fit residues: 19.5173 Evaluate side-chains 59 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 406 GLU 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 471 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** D 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.127516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.101907 restraints weight = 13721.487| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.42 r_work: 0.3701 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4447 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= 0.141 Angle : 0.705 17.530 6705 Z= 0.364 Chirality : 0.047 0.275 734 Planarity : 0.005 0.036 868 Dihedral : 5.411 45.087 683 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.12 % Allowed : 12.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.33), residues: 617 helix: -2.91 (0.70), residues: 22 sheet: -0.48 (0.36), residues: 180 loop : -1.15 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 353 HIS 0.003 0.001 HIS D 198 PHE 0.013 0.001 PHE D 73 TYR 0.013 0.001 TYR D 140 ARG 0.004 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 107) hydrogen bonds : angle 5.44817 ( 324) SS BOND : bond 0.00589 ( 8) SS BOND : angle 3.85116 ( 16) covalent geometry : bond 0.00325 ( 4920) covalent geometry : angle 0.68062 ( 6689) *********************** 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 69 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 205 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8576 (ptpp) REVERT: E 210 LYS cc_start: 0.8120 (mmpt) cc_final: 0.7229 (mmmm) REVERT: D 126 LYS cc_start: 0.1862 (ttpp) cc_final: 0.1427 (ttpp) REVERT: D 183 LYS cc_start: 0.2430 (pttm) cc_final: 0.0337 (pttm) REVERT: A 389 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7644 (p0) REVERT: A 471 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6865 (pm20) outliers start: 22 outliers final: 16 residues processed: 67 average time/residue: 0.2293 time to fit residues: 18.8456 Evaluate side-chains 60 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 367 VAL 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 Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 0.0370 chunk 27 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- 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 A 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.125405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.100950 restraints weight = 13722.718| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.75 r_work: 0.3636 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4928 Z= 0.231 Angle : 0.813 18.848 6705 Z= 0.419 Chirality : 0.050 0.347 734 Planarity : 0.005 0.036 868 Dihedral : 5.897 40.022 683 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.31 % Allowed : 11.99 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.33), residues: 617 helix: -3.15 (0.76), residues: 22 sheet: -0.73 (0.36), residues: 181 loop : -1.23 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 436 HIS 0.005 0.002 HIS D 198 PHE 0.018 0.002 PHE D 73 TYR 0.021 0.002 TYR A 369 ARG 0.004 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 107) hydrogen bonds : angle 6.06905 ( 324) SS BOND : bond 0.01108 ( 8) SS BOND : angle 4.45854 ( 16) covalent geometry : bond 0.00527 ( 4920) covalent geometry : angle 0.78397 ( 6689) *********************** 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 72 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7353 (ttm170) REVERT: D 126 LYS cc_start: 0.2923 (ttpp) cc_final: 0.1680 (ttpp) REVERT: D 183 LYS cc_start: 0.2817 (pttm) cc_final: 0.0875 (pttm) REVERT: A 389 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7717 (p0) outliers start: 23 outliers final: 18 residues processed: 71 average time/residue: 0.2452 time to fit residues: 20.9670 Evaluate side-chains 62 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 86 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 367 VAL 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 Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.128312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.103883 restraints weight = 13725.872| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.84 r_work: 0.3691 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4908 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= 0.129 Angle : 0.717 16.609 6705 Z= 0.370 Chirality : 0.047 0.259 734 Planarity : 0.005 0.039 868 Dihedral : 5.396 47.142 683 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.93 % Allowed : 13.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.33), residues: 617 helix: -2.65 (0.82), residues: 22 sheet: -0.60 (0.36), residues: 181 loop : -1.19 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.003 0.001 HIS D 198 PHE 0.011 0.001 PHE D 73 TYR 0.023 0.001 TYR A 423 ARG 0.005 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 107) hydrogen bonds : angle 5.37491 ( 324) SS BOND : bond 0.00433 ( 8) SS BOND : angle 3.75027 ( 16) covalent geometry : bond 0.00300 ( 4920) covalent geometry : angle 0.69394 ( 6689) *********************** 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 68 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: E 205 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8646 (ptpp) REVERT: E 210 LYS cc_start: 0.8237 (mmpt) cc_final: 0.7778 (mmtt) REVERT: D 126 LYS cc_start: 0.2788 (ttpp) cc_final: 0.1763 (ttpp) REVERT: D 183 LYS cc_start: 0.2467 (pttm) cc_final: 0.0318 (pttm) REVERT: A 389 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7710 (p0) REVERT: A 471 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7139 (pm20) outliers start: 21 outliers final: 16 residues processed: 66 average time/residue: 0.2507 time to fit residues: 20.4439 Evaluate side-chains 61 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 367 VAL 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 Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 0.0070 chunk 60 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.128190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.102781 restraints weight = 13762.023| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.44 r_work: 0.3717 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4986 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= 0.131 Angle : 0.720 15.767 6705 Z= 0.371 Chirality : 0.046 0.241 734 Planarity : 0.005 0.045 868 Dihedral : 5.224 44.571 683 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.93 % Allowed : 13.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.33), residues: 617 helix: -2.57 (0.84), residues: 22 sheet: -0.46 (0.36), residues: 182 loop : -1.17 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 148 HIS 0.003 0.001 HIS D 198 PHE 0.010 0.001 PHE D 73 TYR 0.024 0.002 TYR A 423 ARG 0.005 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 107) hydrogen bonds : angle 5.23566 ( 324) SS BOND : bond 0.00513 ( 8) SS BOND : angle 3.72088 ( 16) covalent geometry : bond 0.00306 ( 4920) covalent geometry : angle 0.69701 ( 6689) ********************** 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 68 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 89 ASP cc_start: 0.7447 (t70) cc_final: 0.7155 (t0) REVERT: E 205 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8773 (ptpp) REVERT: D 126 LYS cc_start: 0.2638 (ttpp) cc_final: 0.1640 (ttpp) REVERT: D 183 LYS cc_start: 0.1888 (pttm) cc_final: -0.0285 (pttm) REVERT: A 389 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7809 (p0) outliers start: 21 outliers final: 18 residues processed: 67 average time/residue: 0.2346 time to fit residues: 19.5677 Evaluate side-chains 63 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 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 367 VAL 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 Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.125000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.101457 restraints weight = 13693.594| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.71 r_work: 0.3642 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 4928 Z= 0.308 Angle : 0.895 17.511 6705 Z= 0.462 Chirality : 0.051 0.295 734 Planarity : 0.006 0.047 868 Dihedral : 6.372 42.389 683 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.12 % Allowed : 13.48 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.33), residues: 617 helix: -2.88 (0.99), residues: 14 sheet: -0.78 (0.37), residues: 181 loop : -1.35 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 148 HIS 0.005 0.002 HIS D 198 PHE 0.023 0.003 PHE D 73 TYR 0.023 0.003 TYR D 140 ARG 0.007 0.001 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 107) hydrogen bonds : angle 6.52863 ( 324) SS BOND : bond 0.00833 ( 8) SS BOND : angle 4.14725 ( 16) covalent geometry : bond 0.00705 ( 4920) covalent geometry : angle 0.87276 ( 6689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.59 seconds wall clock time: 61 minutes 22.42 seconds (3682.42 seconds total)