Starting phenix.real_space_refine on Wed Feb 4 08:59:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qcx_53028/02_2026/9qcx_53028.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qcx_53028/02_2026/9qcx_53028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qcx_53028/02_2026/9qcx_53028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qcx_53028/02_2026/9qcx_53028.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qcx_53028/02_2026/9qcx_53028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qcx_53028/02_2026/9qcx_53028.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 50 5.16 5 C 6221 2.51 5 N 1623 2.21 5 O 1731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9625 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2247 Unusual residues: {'ACE': 1} Classifications: {'peptide': 275, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 260} Chain breaks: 2 Chain: "J" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2468 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 289} Chain breaks: 1 Chain: "K" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2346 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 18, 'TRANS': 273} Chain: "L" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2052 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Time building chain proxies: 1.93, per 1000 atoms: 0.20 Number of scatterers: 9625 At special positions: 0 Unit cell: (84.096, 95.616, 132.48, 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 50 16.00 O 1731 8.00 N 1623 7.00 C 6221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 253.9 milliseconds 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 59.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.635A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 286 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.897A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 removed outlier: 3.722A pdb=" N ASN I 4 " --> pdb=" O MET I 1 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1 through 4' Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 removed outlier: 3.692A pdb=" N LEU I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 removed outlier: 3.631A pdb=" N VAL I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 94 removed outlier: 3.806A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 Processing helix chain 'I' and resid 121 through 128 removed outlier: 3.584A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 154 removed outlier: 4.787A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.508A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.537A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 262 Processing helix chain 'I' and resid 266 through 282 Processing helix chain 'J' and resid 47 through 51 removed outlier: 3.521A pdb=" N ALA J 51 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 removed outlier: 3.657A pdb=" N HIS J 131 " --> pdb=" O TYR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.738A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.982A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 removed outlier: 3.622A pdb=" N LEU J 307 " --> pdb=" O GLY J 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 58 removed outlier: 4.073A pdb=" N GLU K 57 " --> pdb=" O SER K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 94 Processing helix chain 'K' and resid 100 through 121 Processing helix chain 'K' and resid 129 through 131 No H-bonds generated for 'chain 'K' and resid 129 through 131' Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 170 through 175 Processing helix chain 'K' and resid 182 through 199 removed outlier: 3.575A pdb=" N ILE K 186 " --> pdb=" O THR K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 220 Processing helix chain 'K' and resid 229 through 233 Processing helix chain 'K' and resid 247 through 252 removed outlier: 3.998A pdb=" N VAL K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 252 " --> pdb=" O PHE K 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 247 through 252' Processing helix chain 'K' and resid 256 through 267 Processing helix chain 'K' and resid 276 through 282 Processing helix chain 'K' and resid 283 through 287 removed outlier: 3.639A pdb=" N GLN K 287 " --> pdb=" O PRO K 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 193 removed outlier: 4.021A pdb=" N VAL L 191 " --> pdb=" O ARG L 187 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 203 removed outlier: 3.523A pdb=" N LYS L 201 " --> pdb=" O GLY L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 225 Processing helix chain 'L' and resid 228 through 244 removed outlier: 3.522A pdb=" N LEU L 232 " --> pdb=" O GLN L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 269 Processing helix chain 'L' and resid 274 through 282 removed outlier: 3.606A pdb=" N THR L 282 " --> pdb=" O PHE L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 303 Processing helix chain 'L' and resid 310 through 319 Processing helix chain 'L' and resid 320 through 322 No H-bonds generated for 'chain 'L' and resid 320 through 322' Processing helix chain 'L' and resid 326 through 343 removed outlier: 3.792A pdb=" N LEU L 341 " --> pdb=" O GLY L 337 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE L 342 " --> pdb=" O GLU L 338 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP L 343 " --> pdb=" O LEU L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 368 Processing helix chain 'L' and resid 373 through 381 Processing helix chain 'L' and resid 383 through 400 Proline residue: L 389 - end of helix Processing helix chain 'L' and resid 407 through 414 Processing helix chain 'L' and resid 415 through 419 Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.761A pdb=" N LEU L 423 " --> pdb=" O GLY L 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 14 removed outlier: 3.502A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 Processing sheet with id=AA4, first strand: chain 'K' and resid 4 through 12 removed outlier: 6.714A pdb=" N LYS K 20 " --> pdb=" O VAL K 7 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS K 9 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL K 18 " --> pdb=" O LYS K 9 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP K 68 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU K 81 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 85 through 86 removed outlier: 3.836A pdb=" N GLN K 85 " --> pdb=" O ILE K 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 123 through 124 483 hydrogen bonds defined for protein. 1368 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: 1.26 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3071 1.34 - 1.46: 1750 1.46 - 1.57: 4955 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 9857 Sorted by residual: bond pdb=" C ACE I 0 " pdb=" O ACE I 0 " ideal model delta sigma weight residual 1.199 1.226 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" CA VAL K 154 " pdb=" CB VAL K 154 " ideal model delta sigma weight residual 1.546 1.536 0.011 8.80e-03 1.29e+04 1.43e+00 bond pdb=" CB GLU I 182 " pdb=" CG GLU I 182 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.92e-01 bond pdb=" CA VAL K 163 " pdb=" CB VAL K 163 " ideal model delta sigma weight residual 1.540 1.553 -0.013 1.36e-02 5.41e+03 8.49e-01 bond pdb=" CG LEU J 125 " pdb=" CD1 LEU J 125 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.02e-01 ... (remaining 9852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 13034 1.43 - 2.85: 247 2.85 - 4.28: 55 4.28 - 5.71: 12 5.71 - 7.14: 5 Bond angle restraints: 13353 Sorted by residual: angle pdb=" CA GLU I 182 " pdb=" CB GLU I 182 " pdb=" CG GLU I 182 " ideal model delta sigma weight residual 114.10 120.25 -6.15 2.00e+00 2.50e-01 9.44e+00 angle pdb=" C THR L 282 " pdb=" N ASP L 283 " pdb=" CA ASP L 283 " ideal model delta sigma weight residual 122.46 126.69 -4.23 1.41e+00 5.03e-01 9.02e+00 angle pdb=" CA TYR I 91 " pdb=" CB TYR I 91 " pdb=" CG TYR I 91 " ideal model delta sigma weight residual 113.90 109.80 4.10 1.80e+00 3.09e-01 5.18e+00 angle pdb=" CA ILE L 206 " pdb=" CB ILE L 206 " pdb=" CG1 ILE L 206 " ideal model delta sigma weight residual 110.40 114.12 -3.72 1.70e+00 3.46e-01 4.78e+00 angle pdb=" CA VAL K 154 " pdb=" C VAL K 154 " pdb=" N PRO K 155 " ideal model delta sigma weight residual 117.57 119.77 -2.20 1.01e+00 9.80e-01 4.76e+00 ... (remaining 13348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5105 17.55 - 35.11: 612 35.11 - 52.66: 185 52.66 - 70.22: 41 70.22 - 87.77: 21 Dihedral angle restraints: 5964 sinusoidal: 2451 harmonic: 3513 Sorted by residual: dihedral pdb=" CA TYR K 19 " pdb=" C TYR K 19 " pdb=" N LYS K 20 " pdb=" CA LYS K 20 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA THR J 175 " pdb=" C THR J 175 " pdb=" N ARG J 176 " pdb=" CA ARG J 176 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU K 83 " pdb=" C LEU K 83 " pdb=" N HIS K 84 " pdb=" CA HIS K 84 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1052 0.041 - 0.082: 330 0.082 - 0.123: 97 0.123 - 0.164: 12 0.164 - 0.205: 1 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CG LEU H 269 " pdb=" CB LEU H 269 " pdb=" CD1 LEU H 269 " pdb=" CD2 LEU H 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO I 101 " pdb=" N PRO I 101 " pdb=" C PRO I 101 " pdb=" CB PRO I 101 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE K 35 " pdb=" N ILE K 35 " pdb=" C ILE K 35 " pdb=" CB ILE K 35 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 1489 not shown) Planarity restraints: 1695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 110 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO J 111 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO J 111 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 111 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 162 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO I 163 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO I 163 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 163 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY J 200 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C GLY J 200 " -0.026 2.00e-02 2.50e+03 pdb=" O GLY J 200 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS J 201 " 0.009 2.00e-02 2.50e+03 ... (remaining 1692 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1256 2.75 - 3.29: 9060 3.29 - 3.82: 16262 3.82 - 4.36: 19998 4.36 - 4.90: 33565 Nonbonded interactions: 80141 Sorted by model distance: nonbonded pdb=" OH TYR I 86 " pdb=" O LEU I 158 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR L 347 " pdb=" OG1 THR L 397 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR L 238 " pdb=" O LEU L 306 " model vdw 2.278 3.040 nonbonded pdb=" O GLY L 251 " pdb=" OH TYR L 286 " model vdw 2.279 3.040 nonbonded pdb=" OE2 GLU L 230 " pdb=" NE2 GLN L 313 " model vdw 2.288 3.120 ... (remaining 80136 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: 0.430 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.260 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9857 Z= 0.198 Angle : 0.540 7.135 13353 Z= 0.278 Chirality : 0.043 0.205 1492 Planarity : 0.004 0.047 1695 Dihedral : 17.560 87.771 3690 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.80 % Allowed : 22.82 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.25), residues: 1177 helix: 1.98 (0.21), residues: 608 sheet: 0.59 (0.70), residues: 58 loop : -0.11 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 169 TYR 0.022 0.002 TYR I 60 PHE 0.015 0.002 PHE K 152 TRP 0.009 0.001 TRP L 372 HIS 0.003 0.001 HIS J 71 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9857) covalent geometry : angle 0.54035 (13353) hydrogen bonds : bond 0.13347 ( 483) hydrogen bonds : angle 5.43558 ( 1368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: I 275 GLN cc_start: 0.7719 (mm110) cc_final: 0.7028 (mm110) REVERT: J 94 MET cc_start: 0.9179 (mmp) cc_final: 0.8746 (mmp) REVERT: J 233 THR cc_start: 0.8998 (p) cc_final: 0.8775 (p) REVERT: J 298 ARG cc_start: 0.8912 (ttm-80) cc_final: 0.8359 (mtp85) REVERT: J 343 LYS cc_start: 0.8718 (tttt) cc_final: 0.8363 (tttm) REVERT: K 5 GLN cc_start: 0.7911 (tt0) cc_final: 0.7675 (tp-100) REVERT: K 169 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7538 (ttp80) REVERT: L 326 ASN cc_start: 0.7915 (t0) cc_final: 0.7537 (t0) REVERT: L 334 MET cc_start: 0.8774 (tpp) cc_final: 0.8547 (mmm) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.5596 time to fit residues: 79.6206 Evaluate side-chains 135 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 53 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 340 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 169 ARG Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 281 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.074379 restraints weight = 14545.933| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.16 r_work: 0.2757 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9857 Z= 0.153 Angle : 0.503 6.211 13353 Z= 0.262 Chirality : 0.042 0.148 1492 Planarity : 0.004 0.045 1695 Dihedral : 5.495 57.473 1326 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.84 % Allowed : 20.55 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.25), residues: 1177 helix: 2.29 (0.22), residues: 609 sheet: 0.51 (0.65), residues: 58 loop : -0.03 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 197 TYR 0.019 0.001 TYR I 60 PHE 0.017 0.001 PHE K 152 TRP 0.009 0.001 TRP L 372 HIS 0.002 0.001 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9857) covalent geometry : angle 0.50256 (13353) hydrogen bonds : bond 0.04527 ( 483) hydrogen bonds : angle 4.34571 ( 1368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: H 268 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7600 (ttp-170) REVERT: I 28 ARG cc_start: 0.8033 (tmm-80) cc_final: 0.7665 (ttp80) REVERT: I 244 CYS cc_start: 0.8632 (t) cc_final: 0.8255 (t) REVERT: I 275 GLN cc_start: 0.7698 (mm110) cc_final: 0.7008 (mm110) REVERT: J 94 MET cc_start: 0.9189 (mmp) cc_final: 0.8729 (mmp) REVERT: J 188 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8193 (mmm-85) REVERT: J 233 THR cc_start: 0.9032 (p) cc_final: 0.8805 (p) REVERT: J 298 ARG cc_start: 0.8962 (ttm-80) cc_final: 0.8401 (mtp85) REVERT: J 343 LYS cc_start: 0.8737 (tttt) cc_final: 0.8380 (tttm) REVERT: K 5 GLN cc_start: 0.7933 (tt0) cc_final: 0.7693 (tp-100) REVERT: L 250 ARG cc_start: 0.9077 (ptp-170) cc_final: 0.8549 (ptm160) REVERT: L 334 MET cc_start: 0.8833 (tpp) cc_final: 0.8576 (mmm) REVERT: L 415 ASN cc_start: 0.8898 (t0) cc_final: 0.8653 (t0) REVERT: L 417 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8751 (ptmm) outliers start: 30 outliers final: 13 residues processed: 148 average time/residue: 0.5692 time to fit residues: 89.2904 Evaluate side-chains 138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 83 HIS Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 309 ARG Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 417 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 103 optimal weight: 0.0770 chunk 50 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.075291 restraints weight = 14532.853| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.18 r_work: 0.2764 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9857 Z= 0.140 Angle : 0.491 8.026 13353 Z= 0.252 Chirality : 0.042 0.160 1492 Planarity : 0.004 0.045 1695 Dihedral : 4.979 57.073 1308 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.12 % Allowed : 20.83 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.25), residues: 1177 helix: 2.34 (0.21), residues: 611 sheet: 0.54 (0.65), residues: 58 loop : -0.08 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 169 TYR 0.020 0.001 TYR I 60 PHE 0.016 0.001 PHE K 152 TRP 0.008 0.001 TRP L 372 HIS 0.002 0.001 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9857) covalent geometry : angle 0.49083 (13353) hydrogen bonds : bond 0.04170 ( 483) hydrogen bonds : angle 4.18668 ( 1368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: H 268 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7676 (ttp-170) REVERT: I 28 ARG cc_start: 0.8022 (tmm-80) cc_final: 0.7646 (ttp80) REVERT: I 145 GLU cc_start: 0.8311 (tp30) cc_final: 0.7967 (tm-30) REVERT: I 223 ARG cc_start: 0.8829 (ttm110) cc_final: 0.7706 (ttp80) REVERT: I 244 CYS cc_start: 0.8543 (t) cc_final: 0.8198 (t) REVERT: I 275 GLN cc_start: 0.7746 (mm110) cc_final: 0.7028 (mm110) REVERT: J 188 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8167 (mmm-85) REVERT: J 233 THR cc_start: 0.9101 (p) cc_final: 0.8900 (p) REVERT: J 298 ARG cc_start: 0.8995 (ttm-80) cc_final: 0.8409 (mtp85) REVERT: J 343 LYS cc_start: 0.8726 (tttt) cc_final: 0.8384 (tttm) REVERT: K 5 GLN cc_start: 0.7928 (tt0) cc_final: 0.7677 (tp-100) REVERT: K 41 THR cc_start: 0.8052 (p) cc_final: 0.7664 (m) REVERT: L 192 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8769 (mttt) REVERT: L 250 ARG cc_start: 0.9069 (ptp-170) cc_final: 0.8539 (ptm160) REVERT: L 334 MET cc_start: 0.8817 (tpp) cc_final: 0.8553 (mmm) REVERT: L 415 ASN cc_start: 0.8862 (t0) cc_final: 0.8621 (t0) REVERT: L 417 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8816 (ptmm) outliers start: 33 outliers final: 15 residues processed: 152 average time/residue: 0.5995 time to fit residues: 96.6675 Evaluate side-chains 143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 293 LYS Chi-restraints excluded: chain J residue 309 ARG Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 417 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 82 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.104189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.075677 restraints weight = 14749.666| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.21 r_work: 0.2773 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9857 Z= 0.126 Angle : 0.475 6.725 13353 Z= 0.244 Chirality : 0.041 0.160 1492 Planarity : 0.004 0.044 1695 Dihedral : 4.876 56.625 1308 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.65 % Allowed : 21.59 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.25), residues: 1177 helix: 2.43 (0.21), residues: 605 sheet: 0.49 (0.64), residues: 58 loop : -0.05 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 30 TYR 0.019 0.001 TYR I 60 PHE 0.016 0.001 PHE K 152 TRP 0.007 0.001 TRP L 372 HIS 0.002 0.001 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9857) covalent geometry : angle 0.47512 (13353) hydrogen bonds : bond 0.03909 ( 483) hydrogen bonds : angle 4.08471 ( 1368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: H 268 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7682 (ttp-170) REVERT: I 28 ARG cc_start: 0.8025 (tmm-80) cc_final: 0.7661 (ttp80) REVERT: I 145 GLU cc_start: 0.8305 (tp30) cc_final: 0.7959 (tm-30) REVERT: I 223 ARG cc_start: 0.8822 (ttm110) cc_final: 0.7696 (ttp80) REVERT: I 244 CYS cc_start: 0.8553 (t) cc_final: 0.8208 (t) REVERT: I 275 GLN cc_start: 0.7756 (mm110) cc_final: 0.7031 (mm110) REVERT: J 94 MET cc_start: 0.9176 (mmp) cc_final: 0.8913 (mmp) REVERT: J 188 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8197 (mmm-85) REVERT: J 298 ARG cc_start: 0.9000 (ttm-80) cc_final: 0.8417 (mtp85) REVERT: J 343 LYS cc_start: 0.8808 (tttt) cc_final: 0.8497 (tttm) REVERT: K 5 GLN cc_start: 0.8012 (tt0) cc_final: 0.7764 (tp-100) REVERT: K 41 THR cc_start: 0.7974 (p) cc_final: 0.7561 (m) REVERT: L 192 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8742 (mttt) REVERT: L 250 ARG cc_start: 0.9064 (ptp-170) cc_final: 0.8561 (ptm160) REVERT: L 334 MET cc_start: 0.8832 (tpp) cc_final: 0.8568 (mmm) REVERT: L 415 ASN cc_start: 0.8872 (t0) cc_final: 0.8624 (t0) REVERT: L 417 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8823 (ptmm) outliers start: 28 outliers final: 15 residues processed: 149 average time/residue: 0.6031 time to fit residues: 95.3048 Evaluate side-chains 141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 293 LYS Chi-restraints excluded: chain J residue 309 ARG Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 417 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 0.0770 chunk 99 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.104362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.076002 restraints weight = 14614.419| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.18 r_work: 0.2786 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9857 Z= 0.111 Angle : 0.466 6.206 13353 Z= 0.239 Chirality : 0.041 0.157 1492 Planarity : 0.004 0.044 1695 Dihedral : 4.529 55.991 1306 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.75 % Allowed : 21.88 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.25), residues: 1177 helix: 2.50 (0.21), residues: 605 sheet: 0.57 (0.64), residues: 58 loop : -0.04 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 242 TYR 0.018 0.001 TYR I 60 PHE 0.015 0.001 PHE K 152 TRP 0.007 0.001 TRP L 372 HIS 0.002 0.000 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9857) covalent geometry : angle 0.46567 (13353) hydrogen bonds : bond 0.03668 ( 483) hydrogen bonds : angle 4.00847 ( 1368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: H 268 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7669 (ttp-170) REVERT: I 28 ARG cc_start: 0.8046 (tmm-80) cc_final: 0.7694 (ttp80) REVERT: I 145 GLU cc_start: 0.8314 (tp30) cc_final: 0.7951 (tm-30) REVERT: I 152 GLN cc_start: 0.8859 (mt0) cc_final: 0.8364 (tt0) REVERT: I 223 ARG cc_start: 0.8811 (ttm110) cc_final: 0.7680 (ttp80) REVERT: I 244 CYS cc_start: 0.8527 (t) cc_final: 0.8181 (t) REVERT: I 275 GLN cc_start: 0.7734 (mm110) cc_final: 0.6996 (mm110) REVERT: J 298 ARG cc_start: 0.8985 (ttm-80) cc_final: 0.8395 (mtp85) REVERT: J 343 LYS cc_start: 0.8732 (tttt) cc_final: 0.8441 (tttm) REVERT: K 5 GLN cc_start: 0.8039 (tt0) cc_final: 0.7768 (tp-100) REVERT: K 41 THR cc_start: 0.7938 (p) cc_final: 0.7550 (m) REVERT: L 250 ARG cc_start: 0.9062 (ptp-170) cc_final: 0.8548 (ptm160) REVERT: L 317 GLN cc_start: 0.8694 (tp40) cc_final: 0.8080 (mp10) REVERT: L 334 MET cc_start: 0.8801 (tpp) cc_final: 0.8534 (mmm) REVERT: L 415 ASN cc_start: 0.8859 (t0) cc_final: 0.8608 (t0) REVERT: L 417 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8813 (ptmm) outliers start: 29 outliers final: 15 residues processed: 155 average time/residue: 0.5676 time to fit residues: 93.2010 Evaluate side-chains 147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 243 THR Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 293 LYS Chi-restraints excluded: chain J residue 309 ARG Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 417 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 55 optimal weight: 0.0070 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 HIS K 265 GLN ** L 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.073728 restraints weight = 14679.774| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.18 r_work: 0.2749 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9857 Z= 0.210 Angle : 0.541 8.244 13353 Z= 0.274 Chirality : 0.044 0.189 1492 Planarity : 0.004 0.042 1695 Dihedral : 4.633 56.938 1304 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.22 % Allowed : 21.69 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.25), residues: 1177 helix: 2.33 (0.21), residues: 603 sheet: 0.57 (0.66), residues: 58 loop : -0.07 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 242 TYR 0.023 0.002 TYR I 60 PHE 0.015 0.002 PHE K 152 TRP 0.005 0.001 TRP L 372 HIS 0.004 0.001 HIS J 71 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 9857) covalent geometry : angle 0.54081 (13353) hydrogen bonds : bond 0.04526 ( 483) hydrogen bonds : angle 4.18794 ( 1368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: H 268 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7622 (ttp-170) REVERT: I 28 ARG cc_start: 0.8049 (tmm-80) cc_final: 0.7685 (ttp80) REVERT: I 145 GLU cc_start: 0.8303 (tp30) cc_final: 0.7959 (tm-30) REVERT: I 152 GLN cc_start: 0.8897 (mt0) cc_final: 0.8359 (tt0) REVERT: I 223 ARG cc_start: 0.8824 (ttm110) cc_final: 0.7693 (ttp80) REVERT: I 241 ASN cc_start: 0.7817 (t0) cc_final: 0.7193 (t0) REVERT: I 244 CYS cc_start: 0.8461 (t) cc_final: 0.8180 (t) REVERT: I 275 GLN cc_start: 0.7757 (mm110) cc_final: 0.7017 (mm110) REVERT: J 298 ARG cc_start: 0.9037 (ttm-80) cc_final: 0.8436 (mtp85) REVERT: J 343 LYS cc_start: 0.8725 (tttt) cc_final: 0.8377 (tttm) REVERT: K 5 GLN cc_start: 0.8078 (tt0) cc_final: 0.7803 (tp-100) REVERT: K 41 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7552 (m) REVERT: L 326 ASN cc_start: 0.7720 (t0) cc_final: 0.7388 (t160) REVERT: L 415 ASN cc_start: 0.8819 (t0) cc_final: 0.8579 (t0) REVERT: L 417 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8810 (ptmm) outliers start: 34 outliers final: 17 residues processed: 152 average time/residue: 0.6367 time to fit residues: 102.4859 Evaluate side-chains 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 280 CYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 83 HIS Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 293 LYS Chi-restraints excluded: chain J residue 309 ARG Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 250 LYS Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 417 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.075488 restraints weight = 14617.798| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.18 r_work: 0.2775 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9857 Z= 0.119 Angle : 0.490 7.902 13353 Z= 0.250 Chirality : 0.041 0.167 1492 Planarity : 0.004 0.048 1695 Dihedral : 4.497 56.934 1304 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.03 % Allowed : 21.97 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.25), residues: 1177 helix: 2.44 (0.21), residues: 604 sheet: 0.62 (0.64), residues: 58 loop : -0.09 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 30 TYR 0.018 0.001 TYR I 60 PHE 0.016 0.001 PHE K 152 TRP 0.007 0.001 TRP L 372 HIS 0.002 0.001 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9857) covalent geometry : angle 0.49013 (13353) hydrogen bonds : bond 0.03805 ( 483) hydrogen bonds : angle 4.04701 ( 1368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: H 268 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7665 (ttp-170) REVERT: I 28 ARG cc_start: 0.8032 (tmm-80) cc_final: 0.7684 (ttp80) REVERT: I 145 GLU cc_start: 0.8300 (tp30) cc_final: 0.7943 (tm-30) REVERT: I 152 GLN cc_start: 0.8882 (mt0) cc_final: 0.8371 (tt0) REVERT: I 241 ASN cc_start: 0.7816 (t0) cc_final: 0.7189 (t0) REVERT: I 244 CYS cc_start: 0.8411 (t) cc_final: 0.8178 (t) REVERT: I 275 GLN cc_start: 0.7747 (mm110) cc_final: 0.7048 (mm110) REVERT: J 298 ARG cc_start: 0.9014 (ttm-80) cc_final: 0.8422 (mtp85) REVERT: J 343 LYS cc_start: 0.8772 (tttt) cc_final: 0.8459 (tttm) REVERT: K 5 GLN cc_start: 0.8054 (tt0) cc_final: 0.7790 (tp-100) REVERT: K 41 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7546 (m) REVERT: K 59 ASN cc_start: 0.8640 (m-40) cc_final: 0.8344 (m-40) REVERT: L 223 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8490 (mm-30) REVERT: L 250 ARG cc_start: 0.9068 (ptp-170) cc_final: 0.8565 (ptm160) REVERT: L 317 GLN cc_start: 0.8685 (tp40) cc_final: 0.8059 (mp10) REVERT: L 334 MET cc_start: 0.8838 (tpp) cc_final: 0.8602 (mmm) REVERT: L 343 ASP cc_start: 0.8580 (m-30) cc_final: 0.8314 (m-30) REVERT: L 415 ASN cc_start: 0.8872 (t0) cc_final: 0.8635 (t0) REVERT: L 417 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8819 (ptmm) outliers start: 32 outliers final: 17 residues processed: 155 average time/residue: 0.6192 time to fit residues: 101.4943 Evaluate side-chains 151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 280 CYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 417 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 96 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 7 optimal weight: 0.0020 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 HIS K 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.104281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.076020 restraints weight = 14690.707| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.17 r_work: 0.2783 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9857 Z= 0.116 Angle : 0.494 7.551 13353 Z= 0.252 Chirality : 0.041 0.165 1492 Planarity : 0.004 0.047 1695 Dihedral : 4.420 56.218 1304 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.75 % Allowed : 22.35 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.25), residues: 1177 helix: 2.45 (0.21), residues: 604 sheet: 0.58 (0.63), residues: 58 loop : -0.06 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 309 TYR 0.019 0.001 TYR I 60 PHE 0.015 0.001 PHE K 152 TRP 0.007 0.001 TRP L 372 HIS 0.002 0.000 HIS K 84 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9857) covalent geometry : angle 0.49373 (13353) hydrogen bonds : bond 0.03701 ( 483) hydrogen bonds : angle 4.03167 ( 1368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: H 268 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7672 (ttp-170) REVERT: I 28 ARG cc_start: 0.8053 (tmm-80) cc_final: 0.7718 (ttp80) REVERT: I 145 GLU cc_start: 0.8310 (tp30) cc_final: 0.7949 (tm-30) REVERT: I 152 GLN cc_start: 0.8866 (mt0) cc_final: 0.8369 (tt0) REVERT: I 241 ASN cc_start: 0.7809 (t0) cc_final: 0.7185 (t0) REVERT: I 275 GLN cc_start: 0.7741 (mm110) cc_final: 0.6993 (mm110) REVERT: J 298 ARG cc_start: 0.8999 (ttm-80) cc_final: 0.8425 (mtp85) REVERT: J 343 LYS cc_start: 0.8770 (tttt) cc_final: 0.8471 (tttm) REVERT: K 5 GLN cc_start: 0.8056 (tt0) cc_final: 0.7788 (tp-100) REVERT: K 41 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7566 (m) REVERT: L 223 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8448 (mm-30) REVERT: L 250 ARG cc_start: 0.9050 (ptp-170) cc_final: 0.8409 (ptm160) REVERT: L 317 GLN cc_start: 0.8692 (tp40) cc_final: 0.8052 (mp10) REVERT: L 334 MET cc_start: 0.8840 (tpp) cc_final: 0.8630 (mmm) REVERT: L 343 ASP cc_start: 0.8561 (m-30) cc_final: 0.8288 (m-30) REVERT: L 415 ASN cc_start: 0.8876 (t0) cc_final: 0.8625 (t0) REVERT: L 417 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8826 (ptmm) outliers start: 29 outliers final: 17 residues processed: 154 average time/residue: 0.6729 time to fit residues: 109.9205 Evaluate side-chains 151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 280 CYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 293 LYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 417 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 HIS L 296 HIS ** L 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.074248 restraints weight = 14557.466| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.16 r_work: 0.2755 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9857 Z= 0.189 Angle : 0.550 9.460 13353 Z= 0.279 Chirality : 0.044 0.196 1492 Planarity : 0.004 0.046 1695 Dihedral : 4.614 56.789 1304 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.56 % Allowed : 22.63 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.25), residues: 1177 helix: 2.28 (0.21), residues: 603 sheet: 0.50 (0.64), residues: 58 loop : -0.06 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 169 TYR 0.023 0.002 TYR I 60 PHE 0.015 0.001 PHE K 152 TRP 0.006 0.001 TRP L 372 HIS 0.003 0.001 HIS J 71 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9857) covalent geometry : angle 0.55035 (13353) hydrogen bonds : bond 0.04425 ( 483) hydrogen bonds : angle 4.20980 ( 1368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: H 268 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7599 (ttp-170) REVERT: I 28 ARG cc_start: 0.8047 (tmm-80) cc_final: 0.7695 (ttp80) REVERT: I 145 GLU cc_start: 0.8290 (tp30) cc_final: 0.7945 (tm-30) REVERT: I 152 GLN cc_start: 0.8868 (mt0) cc_final: 0.8351 (tt0) REVERT: I 241 ASN cc_start: 0.7827 (t0) cc_final: 0.7207 (t0) REVERT: I 244 CYS cc_start: 0.8388 (t) cc_final: 0.8176 (t) REVERT: I 275 GLN cc_start: 0.7757 (mm110) cc_final: 0.7049 (mm110) REVERT: J 298 ARG cc_start: 0.9027 (ttm-80) cc_final: 0.8427 (mtp85) REVERT: J 343 LYS cc_start: 0.8775 (tttt) cc_final: 0.8427 (tttm) REVERT: K 5 GLN cc_start: 0.8077 (tt0) cc_final: 0.7807 (tp-100) REVERT: K 41 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7589 (m) REVERT: L 223 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8464 (mm-30) REVERT: L 326 ASN cc_start: 0.7714 (t0) cc_final: 0.7414 (t160) REVERT: L 334 MET cc_start: 0.8854 (tpp) cc_final: 0.8581 (mmm) REVERT: L 343 ASP cc_start: 0.8597 (m-30) cc_final: 0.8326 (m-30) REVERT: L 415 ASN cc_start: 0.8882 (t0) cc_final: 0.8638 (t0) REVERT: L 417 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8817 (ptmm) outliers start: 27 outliers final: 17 residues processed: 148 average time/residue: 0.6944 time to fit residues: 108.9440 Evaluate side-chains 149 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 280 CYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 83 HIS Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 HIS K 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.077228 restraints weight = 14529.637| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.17 r_work: 0.2784 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9857 Z= 0.100 Angle : 0.498 10.439 13353 Z= 0.254 Chirality : 0.041 0.186 1492 Planarity : 0.004 0.049 1695 Dihedral : 4.383 56.080 1304 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.08 % Allowed : 22.92 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.25), residues: 1177 helix: 2.47 (0.22), residues: 604 sheet: 0.54 (0.63), residues: 58 loop : -0.06 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 169 TYR 0.019 0.001 TYR I 60 PHE 0.015 0.001 PHE K 152 TRP 0.010 0.001 TRP L 372 HIS 0.002 0.000 HIS L 361 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9857) covalent geometry : angle 0.49807 (13353) hydrogen bonds : bond 0.03505 ( 483) hydrogen bonds : angle 4.05470 ( 1368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: H 268 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7611 (ttp-170) REVERT: I 28 ARG cc_start: 0.8052 (tmm-80) cc_final: 0.7697 (ttp80) REVERT: I 145 GLU cc_start: 0.8348 (tp30) cc_final: 0.7994 (tm-30) REVERT: I 152 GLN cc_start: 0.8879 (mt0) cc_final: 0.8405 (tt0) REVERT: I 241 ASN cc_start: 0.7799 (t0) cc_final: 0.7234 (t0) REVERT: I 275 GLN cc_start: 0.7743 (mm110) cc_final: 0.7039 (mm110) REVERT: J 298 ARG cc_start: 0.8982 (ttm-80) cc_final: 0.8420 (mtp85) REVERT: J 309 ARG cc_start: 0.8483 (mtp-110) cc_final: 0.8207 (mtt-85) REVERT: J 343 LYS cc_start: 0.8860 (tttt) cc_final: 0.8561 (tttm) REVERT: K 5 GLN cc_start: 0.8078 (tt0) cc_final: 0.7804 (tp-100) REVERT: K 41 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7575 (m) REVERT: K 162 GLU cc_start: 0.7212 (pt0) cc_final: 0.6993 (pt0) REVERT: L 223 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8397 (mm-30) REVERT: L 317 GLN cc_start: 0.8676 (tp40) cc_final: 0.8062 (mp10) REVERT: L 334 MET cc_start: 0.8852 (tpp) cc_final: 0.8613 (mmm) REVERT: L 392 MET cc_start: 0.8799 (mtm) cc_final: 0.8440 (pmm) REVERT: L 415 ASN cc_start: 0.8881 (t0) cc_final: 0.8633 (t0) REVERT: L 417 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8840 (ptmm) outliers start: 22 outliers final: 15 residues processed: 152 average time/residue: 0.5865 time to fit residues: 94.8601 Evaluate side-chains 157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 280 CYS Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 83 HIS Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 180 GLU Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 84 HIS ** L 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.074041 restraints weight = 14631.062| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.18 r_work: 0.2728 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9857 Z= 0.240 Angle : 0.598 12.897 13353 Z= 0.301 Chirality : 0.046 0.208 1492 Planarity : 0.004 0.046 1695 Dihedral : 4.686 57.149 1304 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.99 % Allowed : 23.30 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1177 helix: 2.21 (0.21), residues: 603 sheet: 0.46 (0.64), residues: 58 loop : -0.06 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 169 TYR 0.025 0.002 TYR I 60 PHE 0.014 0.002 PHE K 152 TRP 0.006 0.002 TRP J 237 HIS 0.004 0.001 HIS J 71 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 9857) covalent geometry : angle 0.59773 (13353) hydrogen bonds : bond 0.04737 ( 483) hydrogen bonds : angle 4.30932 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.85 seconds wall clock time: 60 minutes 1.86 seconds (3601.86 seconds total)