Starting phenix.real_space_refine on Sat May 10 03:34:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywx_39646/05_2025/8ywx_39646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywx_39646/05_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_39646/05_2025/8ywx_39646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywx_39646/05_2025/8ywx_39646.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywx_39646/05_2025/8ywx_39646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywx_39646/05_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-5687/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: 4.15, per 1000 atoms: 0.86 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: 1.11 Conformation dependent library (CDL) restraints added in 585.3 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: 0.67 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: 1.35 Time building geometry restraints manager: 1.33 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: 7.980 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.990 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- 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 (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 : 0.587 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: 0.2154 time to fit residues: 23.0771 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 : 0.510 ------------------------------------------------------------------------------- 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: 0.5980 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.130712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.104392 restraints weight = 13708.539| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.38 r_work: 0.3760 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2501 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= 0.137 Angle : 0.661 7.812 6705 Z= 0.354 Chirality : 0.048 0.217 734 Planarity : 0.006 0.062 868 Dihedral : 6.486 53.614 694 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.81 % Allowed : 9.74 % Favored : 87.45 % 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: -1.37 (0.33), residues: 617 helix: -1.85 (0.94), residues: 21 sheet: -0.21 (0.38), residues: 173 loop : -1.21 (0.30), residues: 423 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 0.024 0.002 PHE A 377 TYR 0.016 0.002 TYR D 140 ARG 0.005 0.000 ARG E 71 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 107) hydrogen bonds : angle 6.39985 ( 324) SS BOND : bond 0.00770 ( 8) SS BOND : angle 2.26325 ( 16) covalent geometry : bond 0.00306 ( 4920) covalent geometry : angle 0.65245 ( 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 : 0.554 Fit side-chains revert: symmetry clash REVERT: E 203 ASN cc_start: 0.7410 (m-40) cc_final: 0.7016 (m110) REVERT: E 210 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8264 (mmmt) outliers start: 15 outliers final: 8 residues processed: 72 average time/residue: 0.1826 time to fit residues: 16.7321 Evaluate side-chains 53 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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: 5.9990 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 53 optimal weight: 0.0670 chunk 32 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.127064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.099963 restraints weight = 13163.823| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 4.14 r_work: 0.3587 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4928 Z= 0.158 Angle : 0.684 13.783 6705 Z= 0.363 Chirality : 0.047 0.299 734 Planarity : 0.006 0.053 868 Dihedral : 5.511 44.106 683 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.56 % Allowed : 10.30 % Favored : 86.14 % 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: -1.98 (0.97), residues: 20 sheet: -0.34 (0.38), residues: 176 loop : -1.27 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 436 HIS 0.002 0.001 HIS E 102 PHE 0.020 0.002 PHE A 377 TYR 0.015 0.002 TYR A 369 ARG 0.003 0.000 ARG E 31 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 107) hydrogen bonds : angle 5.92210 ( 324) SS BOND : bond 0.00926 ( 8) SS BOND : angle 3.34390 ( 16) covalent geometry : bond 0.00358 ( 4920) covalent geometry : angle 0.66541 ( 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 79 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 203 ASN cc_start: 0.7561 (m-40) cc_final: 0.7258 (m110) REVERT: E 210 LYS cc_start: 0.8657 (mmpt) cc_final: 0.8314 (mmmm) REVERT: D 183 LYS cc_start: 0.1428 (pttm) cc_final: 0.0252 (ptmt) REVERT: A 389 ASP cc_start: 0.8810 (m-30) cc_final: 0.8496 (p0) outliers start: 19 outliers final: 9 residues processed: 75 average time/residue: 0.2550 time to fit residues: 23.5522 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 : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL 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 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.128784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.103846 restraints weight = 13944.708| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.81 r_work: 0.3719 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4928 Z= 0.122 Angle : 0.721 24.147 6705 Z= 0.368 Chirality : 0.048 0.377 734 Planarity : 0.005 0.045 868 Dihedral : 5.200 47.819 683 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.81 % Allowed : 12.36 % 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: -1.34 (0.33), residues: 617 helix: -1.60 (1.20), residues: 14 sheet: -0.11 (0.39), residues: 172 loop : -1.27 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.002 0.001 HIS E 102 PHE 0.014 0.001 PHE A 377 TYR 0.018 0.001 TYR A 423 ARG 0.002 0.000 ARG E 31 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 107) hydrogen bonds : angle 5.28723 ( 324) SS BOND : bond 0.01050 ( 8) SS BOND : angle 4.15999 ( 16) covalent geometry : bond 0.00271 ( 4920) covalent geometry : angle 0.69263 ( 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 65 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: E 203 ASN cc_start: 0.7787 (m-40) cc_final: 0.7455 (m110) REVERT: E 205 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8580 (ptpp) REVERT: E 210 LYS cc_start: 0.8617 (mmpt) cc_final: 0.8005 (mmmt) REVERT: D 105 GLU cc_start: 0.7845 (mp0) cc_final: 0.7634 (pm20) REVERT: D 126 LYS cc_start: 0.2861 (tptm) cc_final: 0.2279 (tmtt) REVERT: D 183 LYS cc_start: 0.1455 (pttm) cc_final: 0.0394 (pttm) REVERT: A 389 ASP cc_start: 0.8411 (m-30) cc_final: 0.8157 (p0) REVERT: A 465 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6775 (tm-30) REVERT: A 471 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7177 (pm20) outliers start: 15 outliers final: 7 residues processed: 63 average time/residue: 0.2074 time to fit residues: 16.5283 Evaluate side-chains 52 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 0.0970 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: 0.5980 chunk 6 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.125981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.099990 restraints weight = 13942.589| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.37 r_work: 0.3677 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4928 Z= 0.206 Angle : 0.758 17.440 6705 Z= 0.396 Chirality : 0.049 0.348 734 Planarity : 0.005 0.043 868 Dihedral : 5.452 43.188 681 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.62 % Allowed : 13.67 % 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: -1.52 (0.33), residues: 617 helix: -2.51 (0.99), residues: 14 sheet: -0.41 (0.37), residues: 182 loop : -1.29 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.004 0.001 HIS D 198 PHE 0.019 0.002 PHE D 73 TYR 0.018 0.002 TYR D 140 ARG 0.004 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 107) hydrogen bonds : angle 5.91083 ( 324) SS BOND : bond 0.00753 ( 8) SS BOND : angle 4.02315 ( 16) covalent geometry : bond 0.00468 ( 4920) covalent geometry : angle 0.73285 ( 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 65 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 203 ASN cc_start: 0.7826 (m-40) cc_final: 0.7545 (m110) REVERT: E 210 LYS cc_start: 0.8534 (mmpt) cc_final: 0.8181 (mmmm) REVERT: D 183 LYS cc_start: 0.2539 (pttm) cc_final: 0.0583 (pttm) REVERT: A 389 ASP cc_start: 0.8625 (m-30) cc_final: 0.8278 (p0) REVERT: A 465 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6710 (tm-30) outliers start: 14 outliers final: 11 residues processed: 64 average time/residue: 0.2301 time to fit residues: 17.9210 Evaluate side-chains 53 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 0.0670 chunk 54 optimal weight: 0.6980 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.129069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.106712 restraints weight = 13810.785| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.65 r_work: 0.3734 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4134 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= 0.124 Angle : 0.671 13.044 6705 Z= 0.347 Chirality : 0.046 0.260 734 Planarity : 0.005 0.038 868 Dihedral : 4.912 33.744 681 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.81 % Allowed : 15.17 % 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 (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: -2.69 (0.77), residues: 22 sheet: -0.39 (0.36), residues: 182 loop : -1.26 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.003 0.001 HIS D 198 PHE 0.010 0.001 PHE D 73 TYR 0.019 0.001 TYR A 423 ARG 0.004 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 107) hydrogen bonds : angle 5.31882 ( 324) SS BOND : bond 0.00480 ( 8) SS BOND : angle 3.45206 ( 16) covalent geometry : bond 0.00286 ( 4920) covalent geometry : angle 0.64983 ( 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 62 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.521 Fit side-chains REVERT: E 203 ASN cc_start: 0.7713 (m-40) cc_final: 0.7355 (m-40) REVERT: E 205 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8479 (mttp) REVERT: E 210 LYS cc_start: 0.8594 (mmpt) cc_final: 0.7908 (mmmm) REVERT: D 183 LYS cc_start: 0.2229 (pttm) cc_final: -0.0021 (pttt) REVERT: A 389 ASP cc_start: 0.8385 (m-30) cc_final: 0.8106 (p0) REVERT: A 465 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6768 (tm-30) outliers start: 15 outliers final: 13 residues processed: 61 average time/residue: 0.2046 time to fit residues: 15.5856 Evaluate side-chains 55 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4290 r_free = 0.4290 target = 0.127319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.103229 restraints weight = 13714.726| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.73 r_work: 0.3688 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4342 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= 0.156 Angle : 0.720 18.667 6705 Z= 0.371 Chirality : 0.048 0.297 734 Planarity : 0.005 0.036 868 Dihedral : 5.096 38.619 681 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.56 % Allowed : 14.04 % Favored : 82.40 % 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: -2.80 (0.73), residues: 22 sheet: -0.42 (0.36), residues: 181 loop : -1.23 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS D 198 PHE 0.014 0.001 PHE D 73 TYR 0.017 0.002 TYR A 369 ARG 0.003 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 107) hydrogen bonds : angle 5.46123 ( 324) SS BOND : bond 0.00524 ( 8) SS BOND : angle 3.71160 ( 16) covalent geometry : bond 0.00362 ( 4920) covalent geometry : angle 0.69716 ( 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 68 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: E 205 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8614 (mttp) REVERT: E 210 LYS cc_start: 0.8520 (mmpt) cc_final: 0.7986 (mmmm) REVERT: D 126 LYS cc_start: 0.1610 (ttpp) cc_final: 0.0542 (ttpp) REVERT: D 183 LYS cc_start: 0.2404 (pttm) cc_final: 0.0033 (pttt) REVERT: A 389 ASP cc_start: 0.8589 (m-30) cc_final: 0.8189 (p0) outliers start: 19 outliers final: 16 residues processed: 67 average time/residue: 0.2351 time to fit residues: 19.2142 Evaluate side-chains 59 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 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 471 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.127886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.103714 restraints weight = 13640.688| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.77 r_work: 0.3682 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4928 Z= 0.156 Angle : 0.738 17.677 6705 Z= 0.379 Chirality : 0.048 0.319 734 Planarity : 0.005 0.036 868 Dihedral : 5.122 35.849 681 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.75 % Allowed : 14.42 % Favored : 81.84 % 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: -1.49 (0.33), residues: 617 helix: -2.60 (0.84), residues: 22 sheet: -0.45 (0.36), residues: 181 loop : -1.18 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS D 198 PHE 0.015 0.001 PHE D 73 TYR 0.016 0.002 TYR A 423 ARG 0.003 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 107) hydrogen bonds : angle 5.42717 ( 324) SS BOND : bond 0.00648 ( 8) SS BOND : angle 4.14622 ( 16) covalent geometry : bond 0.00355 ( 4920) covalent geometry : angle 0.71020 ( 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 77 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: E 210 LYS cc_start: 0.8191 (mmpt) cc_final: 0.7784 (mmmm) REVERT: D 126 LYS cc_start: 0.1328 (ttpp) cc_final: 0.0166 (ptmm) REVERT: D 183 LYS cc_start: 0.2511 (pttm) cc_final: 0.0088 (pttt) REVERT: A 389 ASP cc_start: 0.8588 (m-30) cc_final: 0.8188 (p0) outliers start: 20 outliers final: 16 residues processed: 73 average time/residue: 0.2534 time to fit residues: 22.0338 Evaluate side-chains 63 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 471 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.128524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.104215 restraints weight = 13709.762| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 3.90 r_work: 0.3705 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4928 Z= 0.141 Angle : 0.753 15.529 6705 Z= 0.385 Chirality : 0.047 0.287 734 Planarity : 0.005 0.035 868 Dihedral : 5.006 36.441 681 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.93 % Allowed : 14.04 % Favored : 82.02 % 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: -1.44 (0.33), residues: 617 helix: -2.53 (0.86), residues: 22 sheet: -0.42 (0.37), residues: 181 loop : -1.14 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.003 0.001 HIS D 198 PHE 0.013 0.001 PHE D 73 TYR 0.015 0.001 TYR A 423 ARG 0.003 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 107) hydrogen bonds : angle 5.34188 ( 324) SS BOND : bond 0.00513 ( 8) SS BOND : angle 3.96151 ( 16) covalent geometry : bond 0.00328 ( 4920) covalent geometry : angle 0.72887 ( 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 69 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: E 86 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7279 (ttm170) REVERT: E 205 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8487 (mttp) REVERT: E 210 LYS cc_start: 0.8149 (mmpt) cc_final: 0.7555 (mmmm) REVERT: D 126 LYS cc_start: 0.1134 (ttpp) cc_final: -0.0210 (ttpp) REVERT: D 183 LYS cc_start: 0.2161 (pttm) cc_final: 0.0072 (pttm) REVERT: A 389 ASP cc_start: 0.8500 (m-30) cc_final: 0.8131 (p0) outliers start: 21 outliers final: 18 residues processed: 68 average time/residue: 0.2254 time to fit residues: 18.8758 Evaluate side-chains 64 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 101 ARG 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 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: 0.0060 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 17 optimal weight: 0.0470 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 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 = 0.4335 r_free = 0.4335 target = 0.130656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.107219 restraints weight = 13743.323| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 3.85 r_work: 0.3763 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4907 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= 0.120 Angle : 0.707 13.508 6705 Z= 0.363 Chirality : 0.046 0.260 734 Planarity : 0.005 0.042 868 Dihedral : 4.745 37.287 681 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.00 % Allowed : 15.17 % Favored : 81.84 % 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: -1.28 (0.34), residues: 617 helix: -2.55 (0.85), residues: 24 sheet: -0.09 (0.37), residues: 176 loop : -1.13 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 353 HIS 0.002 0.001 HIS D 198 PHE 0.009 0.001 PHE D 73 TYR 0.013 0.001 TYR A 423 ARG 0.003 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 107) hydrogen bonds : angle 4.91855 ( 324) SS BOND : bond 0.00279 ( 8) SS BOND : angle 3.67022 ( 16) covalent geometry : bond 0.00280 ( 4920) covalent geometry : angle 0.68462 ( 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 69 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: E 205 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8444 (mttp) REVERT: E 210 LYS cc_start: 0.8172 (mmpt) cc_final: 0.7498 (mmmm) REVERT: D 126 LYS cc_start: 0.0950 (ttpp) cc_final: -0.0912 (tttm) REVERT: D 183 LYS cc_start: 0.2167 (pttm) cc_final: 0.0130 (pttm) REVERT: A 389 ASP cc_start: 0.8476 (m-30) cc_final: 0.8135 (p0) outliers start: 16 outliers final: 14 residues processed: 68 average time/residue: 0.2354 time to fit residues: 19.6522 Evaluate side-chains 63 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 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 101 ARG 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 350 VAL Chi-restraints excluded: chain A residue 367 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.129632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.105965 restraints weight = 13851.526| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 3.64 r_work: 0.3741 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4928 Z= 0.137 Angle : 0.734 14.004 6705 Z= 0.375 Chirality : 0.046 0.260 734 Planarity : 0.005 0.048 868 Dihedral : 4.800 34.972 681 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.00 % Allowed : 14.98 % 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 (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: -1.32 (0.34), residues: 617 helix: -2.67 (0.84), residues: 24 sheet: -0.33 (0.37), residues: 183 loop : -1.04 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS D 198 PHE 0.012 0.001 PHE D 73 TYR 0.019 0.001 TYR D 173 ARG 0.005 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 107) hydrogen bonds : angle 5.09455 ( 324) SS BOND : bond 0.00408 ( 8) SS BOND : angle 3.80941 ( 16) covalent geometry : bond 0.00322 ( 4920) covalent geometry : angle 0.71051 ( 6689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.14 seconds wall clock time: 54 minutes 59.42 seconds (3299.42 seconds total)