Starting phenix.real_space_refine on Sun Apr 5 01:27:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r4y_53572/04_2026/9r4y_53572.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r4y_53572/04_2026/9r4y_53572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r4y_53572/04_2026/9r4y_53572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r4y_53572/04_2026/9r4y_53572.map" model { file = "/net/cci-nas-00/data/ceres_data/9r4y_53572/04_2026/9r4y_53572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r4y_53572/04_2026/9r4y_53572.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 4218 2.51 5 N 1148 2.21 5 O 1296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6726 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3321 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 408} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3339 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 406} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.55, per 1000 atoms: 0.23 Number of scatterers: 6726 At special positions: 0 Unit cell: (67.221, 70.422, 109.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 6 15.00 Mg 2 11.99 O 1296 8.00 N 1148 7.00 C 4218 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: 0.58 Conformation dependent library (CDL) restraints added in 269.0 milliseconds 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 53.8% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.649A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 removed outlier: 4.237A pdb=" N THR A 51 " --> pdb=" O ALA A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.565A pdb=" N VAL A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 4.655A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.610A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.153A pdb=" N HIS A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.031A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.107A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.937A pdb=" N VAL A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.024A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 4.173A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.053A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.483A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 108 through 126 removed outlier: 5.173A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ALA B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.633A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.598A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.735A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.793A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.692A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.660A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.037A pdb=" N MET B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 381 " --> pdb=" O MET B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.082A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 removed outlier: 3.571A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.767A pdb=" N ILE A 93 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL A 66 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N MET A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N CYS A 171 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N SER A 139 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS A 166 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN A 168 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 204 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS A 170 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA A 201 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.694A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N CYS A 315 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.907A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N MET B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN B 8 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU B 3 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLN B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL B 5 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR B 136 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 7 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLU B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE B 133 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 169 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE B 268 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL B 201 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 10.551A pdb=" N PHE B 270 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 14.005A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 369 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 313 hydrogen bonds defined for protein. 900 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: 1.13 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2237 1.35 - 1.47: 1635 1.47 - 1.59: 2903 1.59 - 1.72: 8 1.72 - 1.84: 90 Bond restraints: 6873 Sorted by residual: bond pdb=" C GLU A 71 " pdb=" N PRO A 72 " ideal model delta sigma weight residual 1.334 1.323 0.010 8.40e-03 1.42e+04 1.49e+00 bond pdb=" C ALA A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.47e+00 bond pdb=" C GLY B 93 " pdb=" N GLN B 94 " ideal model delta sigma weight residual 1.332 1.319 0.013 1.40e-02 5.10e+03 8.99e-01 bond pdb=" CA PRO A 359 " pdb=" C PRO A 359 " ideal model delta sigma weight residual 1.517 1.522 -0.005 6.70e-03 2.23e+04 5.28e-01 bond pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " ideal model delta sigma weight residual 1.524 1.512 0.012 2.00e-02 2.50e+03 3.73e-01 ... (remaining 6868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 8998 1.07 - 2.14: 257 2.14 - 3.21: 48 3.21 - 4.28: 14 4.28 - 5.35: 6 Bond angle restraints: 9323 Sorted by residual: angle pdb=" N ALA A 273 " pdb=" CA ALA A 273 " pdb=" C ALA A 273 " ideal model delta sigma weight residual 109.81 114.58 -4.77 2.21e+00 2.05e-01 4.67e+00 angle pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 111.00 105.65 5.35 3.00e+00 1.11e-01 3.18e+00 angle pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " ideal model delta sigma weight residual 111.00 105.66 5.34 3.00e+00 1.11e-01 3.17e+00 angle pdb=" CA TRP A 21 " pdb=" CB TRP A 21 " pdb=" CG TRP A 21 " ideal model delta sigma weight residual 113.60 110.38 3.22 1.90e+00 2.77e-01 2.87e+00 angle pdb=" C LYS A 311 " pdb=" N TYR A 312 " pdb=" CA TYR A 312 " ideal model delta sigma weight residual 120.87 118.48 2.39 1.42e+00 4.96e-01 2.84e+00 ... (remaining 9318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 4070 35.73 - 71.47: 34 71.47 - 107.20: 2 107.20 - 142.93: 2 142.93 - 178.66: 2 Dihedral angle restraints: 4110 sinusoidal: 1657 harmonic: 2453 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -76.74 -178.66 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2G GTP A 501 " pdb=" O3B GTP A 501 " pdb=" PG GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 177.30 5.09 172.21 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O3B GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 291.08 152.31 138.77 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 4107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 753 0.044 - 0.088: 199 0.088 - 0.132: 61 0.132 - 0.176: 2 0.176 - 0.220: 1 Chirality restraints: 1016 Sorted by residual: chirality pdb=" CG LEU A 397 " pdb=" CB LEU A 397 " pdb=" CD1 LEU A 397 " pdb=" CD2 LEU A 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CG LEU A 286 " pdb=" CB LEU A 286 " pdb=" CD1 LEU A 286 " pdb=" CD2 LEU A 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CG LEU A 368 " pdb=" CB LEU A 368 " pdb=" CD1 LEU A 368 " pdb=" CD2 LEU A 368 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1013 not shown) Planarity restraints: 1214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 174 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 175 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 79 " 0.108 9.50e-02 1.11e+02 4.96e-02 2.85e+00 pdb=" NE ARG A 79 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG A 79 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 79 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 79 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 103 " 0.005 2.00e-02 2.50e+03 1.15e-02 2.33e+00 pdb=" CG PHE A 103 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 103 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 103 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 103 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 103 " 0.021 2.00e-02 2.50e+03 ... (remaining 1211 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 32 2.45 - 3.06: 4513 3.06 - 3.68: 10219 3.68 - 4.29: 15831 4.29 - 4.90: 26584 Nonbonded interactions: 57179 Sorted by model distance: nonbonded pdb=" O2G G2P B 501 " pdb="MG MG B 502 " model vdw 1.841 2.170 nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 1.843 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.952 2.170 nonbonded pdb=" O2B G2P B 501 " pdb="MG MG B 502 " model vdw 1.974 2.170 nonbonded pdb=" O LEU A 194 " pdb=" OG1 THR A 198 " model vdw 2.196 3.040 ... (remaining 57174 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: 12.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.830 Find NCS groups from input model: 0.030 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.003 0.028 6873 Z= 0.138 Angle : 0.478 5.348 9323 Z= 0.249 Chirality : 0.042 0.220 1016 Planarity : 0.005 0.055 1214 Dihedral : 12.060 178.665 2536 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.38 % Allowed : 3.73 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.86 (0.30), residues: 847 helix: 1.85 (0.28), residues: 372 sheet: 0.34 (0.48), residues: 131 loop : -0.76 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 79 TYR 0.022 0.001 TYR A 282 PHE 0.021 0.002 PHE A 103 TRP 0.015 0.002 TRP A 21 HIS 0.006 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6873) covalent geometry : angle 0.47767 ( 9323) hydrogen bonds : bond 0.15408 ( 313) hydrogen bonds : angle 6.52501 ( 900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.255 Fit side-chains REVERT: A 35 GLN cc_start: 0.7578 (mt0) cc_final: 0.7326 (mm-40) REVERT: A 50 ASN cc_start: 0.7700 (t0) cc_final: 0.7212 (t0) REVERT: A 90 GLU cc_start: 0.7537 (tt0) cc_final: 0.7127 (tm-30) REVERT: A 251 ASP cc_start: 0.6894 (t0) cc_final: 0.6498 (m-30) REVERT: B 66 MET cc_start: 0.8143 (ttp) cc_final: 0.7858 (ttt) REVERT: B 177 ASP cc_start: 0.8452 (t0) cc_final: 0.8208 (t0) REVERT: B 238 CYS cc_start: 0.7609 (p) cc_final: 0.7298 (p) REVERT: B 280 GLN cc_start: 0.8845 (mt0) cc_final: 0.8220 (pt0) REVERT: B 299 MET cc_start: 0.7346 (mtm) cc_final: 0.7015 (mmp) REVERT: B 321 MET cc_start: 0.8797 (ptp) cc_final: 0.8281 (ptp) REVERT: B 362 LYS cc_start: 0.7715 (pttp) cc_final: 0.7179 (pttp) REVERT: B 405 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7464 (tm-30) outliers start: 10 outliers final: 5 residues processed: 114 average time/residue: 0.6931 time to fit residues: 82.4696 Evaluate side-chains 80 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 348 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.101017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083494 restraints weight = 9946.323| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.27 r_work: 0.3202 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6873 Z= 0.149 Angle : 0.523 7.735 9323 Z= 0.271 Chirality : 0.043 0.149 1016 Planarity : 0.004 0.056 1214 Dihedral : 12.905 179.563 978 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.21 % Allowed : 9.39 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.78 (0.29), residues: 847 helix: 1.70 (0.28), residues: 381 sheet: 0.28 (0.47), residues: 129 loop : -0.74 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 390 TYR 0.011 0.001 TYR B 159 PHE 0.028 0.001 PHE A 255 TRP 0.015 0.002 TRP A 21 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6873) covalent geometry : angle 0.52317 ( 9323) hydrogen bonds : bond 0.04220 ( 313) hydrogen bonds : angle 4.72439 ( 900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.282 Fit side-chains REVERT: A 50 ASN cc_start: 0.8633 (t0) cc_final: 0.8265 (t0) REVERT: A 91 GLN cc_start: 0.7859 (mt0) cc_final: 0.7580 (mt0) REVERT: B 118 ASP cc_start: 0.8196 (t0) cc_final: 0.7949 (t0) REVERT: B 276 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7192 (OUTLIER) REVERT: B 321 MET cc_start: 0.8513 (ptp) cc_final: 0.7748 (ptp) REVERT: B 363 MET cc_start: 0.8566 (ptm) cc_final: 0.8303 (ptp) REVERT: B 405 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7709 (tm-30) REVERT: B 406 MET cc_start: 0.7891 (pp-130) cc_final: 0.7689 (pp-130) outliers start: 16 outliers final: 7 residues processed: 95 average time/residue: 0.6164 time to fit residues: 61.6174 Evaluate side-chains 77 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 348 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** 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 = 0.3629 r_free = 0.3629 target = 0.101436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083786 restraints weight = 9702.215| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.26 r_work: 0.3197 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6873 Z= 0.137 Angle : 0.505 6.616 9323 Z= 0.262 Chirality : 0.042 0.137 1016 Planarity : 0.004 0.034 1214 Dihedral : 12.749 179.371 976 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.07 % Allowed : 10.91 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.73 (0.29), residues: 847 helix: 1.70 (0.28), residues: 380 sheet: 0.19 (0.48), residues: 129 loop : -0.78 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 390 TYR 0.010 0.001 TYR B 159 PHE 0.030 0.001 PHE A 255 TRP 0.015 0.002 TRP A 21 HIS 0.002 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6873) covalent geometry : angle 0.50535 ( 9323) hydrogen bonds : bond 0.03948 ( 313) hydrogen bonds : angle 4.55080 ( 900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.284 Fit side-chains REVERT: A 50 ASN cc_start: 0.8641 (t0) cc_final: 0.8305 (t0) REVERT: A 91 GLN cc_start: 0.7512 (mt0) cc_final: 0.7290 (mt0) REVERT: B 118 ASP cc_start: 0.8144 (t0) cc_final: 0.7944 (t0) REVERT: B 321 MET cc_start: 0.8477 (ptp) cc_final: 0.7837 (ptp) REVERT: B 363 MET cc_start: 0.8626 (ptm) cc_final: 0.8382 (ptp) outliers start: 15 outliers final: 6 residues processed: 80 average time/residue: 0.5766 time to fit residues: 48.8559 Evaluate side-chains 74 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 348 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** 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 = 0.3609 r_free = 0.3609 target = 0.099886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081985 restraints weight = 9977.330| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.30 r_work: 0.3170 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6873 Z= 0.165 Angle : 0.524 7.512 9323 Z= 0.270 Chirality : 0.042 0.136 1016 Planarity : 0.004 0.034 1214 Dihedral : 12.786 179.674 976 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.62 % Allowed : 11.05 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.58 (0.29), residues: 847 helix: 1.56 (0.27), residues: 381 sheet: 0.05 (0.47), residues: 129 loop : -0.82 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.011 0.001 TYR B 159 PHE 0.032 0.002 PHE A 255 TRP 0.015 0.002 TRP A 21 HIS 0.003 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6873) covalent geometry : angle 0.52357 ( 9323) hydrogen bonds : bond 0.04153 ( 313) hydrogen bonds : angle 4.50352 ( 900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.266 Fit side-chains REVERT: A 50 ASN cc_start: 0.8655 (t0) cc_final: 0.8327 (t0) REVERT: A 137 MET cc_start: 0.8530 (tpp) cc_final: 0.8206 (tpp) REVERT: A 301 MET cc_start: 0.8158 (mmp) cc_final: 0.7880 (mmp) REVERT: A 377 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8749 (tmm) REVERT: A 415 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: B 165 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8771 (pt0) REVERT: B 321 MET cc_start: 0.8470 (ptp) cc_final: 0.7832 (ptp) outliers start: 19 outliers final: 10 residues processed: 87 average time/residue: 0.5240 time to fit residues: 48.2715 Evaluate side-chains 80 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 35 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** B 8 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 = 0.3665 r_free = 0.3665 target = 0.103815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086021 restraints weight = 9828.786| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.29 r_work: 0.3238 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6873 Z= 0.092 Angle : 0.474 5.930 9323 Z= 0.245 Chirality : 0.040 0.134 1016 Planarity : 0.004 0.034 1214 Dihedral : 12.505 178.840 976 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.80 % Allowed : 12.29 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.79 (0.30), residues: 847 helix: 1.86 (0.28), residues: 382 sheet: -0.04 (0.48), residues: 129 loop : -0.81 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 306 TYR 0.007 0.001 TYR B 310 PHE 0.029 0.001 PHE A 255 TRP 0.016 0.002 TRP A 21 HIS 0.002 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 6873) covalent geometry : angle 0.47398 ( 9323) hydrogen bonds : bond 0.03180 ( 313) hydrogen bonds : angle 4.20138 ( 900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.283 Fit side-chains REVERT: A 50 ASN cc_start: 0.8550 (t0) cc_final: 0.8255 (t0) REVERT: A 279 GLU cc_start: 0.7821 (pm20) cc_final: 0.7613 (pm20) REVERT: A 415 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: B 165 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8704 (pt0) REVERT: B 212 PHE cc_start: 0.7332 (m-10) cc_final: 0.7039 (m-10) REVERT: B 321 MET cc_start: 0.8246 (ptp) cc_final: 0.7877 (ptp) REVERT: B 347 HIS cc_start: 0.7222 (t-90) cc_final: 0.6926 (t70) outliers start: 13 outliers final: 6 residues processed: 84 average time/residue: 0.5279 time to fit residues: 46.9965 Evaluate side-chains 80 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 348 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** 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 = 0.3639 r_free = 0.3639 target = 0.102046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084265 restraints weight = 9870.010| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.29 r_work: 0.3207 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6873 Z= 0.128 Angle : 0.505 6.008 9323 Z= 0.260 Chirality : 0.041 0.132 1016 Planarity : 0.003 0.034 1214 Dihedral : 12.539 178.130 975 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.93 % Allowed : 12.29 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.74 (0.29), residues: 847 helix: 1.79 (0.28), residues: 382 sheet: -0.04 (0.47), residues: 129 loop : -0.80 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 306 TYR 0.009 0.001 TYR B 159 PHE 0.030 0.001 PHE A 255 TRP 0.012 0.001 TRP A 21 HIS 0.002 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6873) covalent geometry : angle 0.50457 ( 9323) hydrogen bonds : bond 0.03567 ( 313) hydrogen bonds : angle 4.23842 ( 900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.261 Fit side-chains REVERT: A 50 ASN cc_start: 0.8575 (t0) cc_final: 0.8263 (t0) REVERT: A 137 MET cc_start: 0.8464 (tpp) cc_final: 0.8219 (tpp) REVERT: A 279 GLU cc_start: 0.7891 (pm20) cc_final: 0.7662 (pm20) REVERT: A 415 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: B 165 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8803 (pt0) REVERT: B 212 PHE cc_start: 0.7412 (m-10) cc_final: 0.7142 (m-10) REVERT: B 321 MET cc_start: 0.8294 (ptp) cc_final: 0.7940 (ptp) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.5651 time to fit residues: 50.8820 Evaluate side-chains 84 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** B 8 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 = 0.3573 r_free = 0.3573 target = 0.097863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080204 restraints weight = 9924.754| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.27 r_work: 0.3135 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6873 Z= 0.257 Angle : 0.620 9.527 9323 Z= 0.322 Chirality : 0.045 0.128 1016 Planarity : 0.004 0.035 1214 Dihedral : 12.560 177.256 971 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.49 % Allowed : 13.12 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.22 (0.29), residues: 847 helix: 1.27 (0.27), residues: 382 sheet: -0.25 (0.47), residues: 136 loop : -0.97 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 306 TYR 0.015 0.002 TYR B 159 PHE 0.031 0.002 PHE A 255 TRP 0.013 0.002 TRP A 21 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00601 ( 6873) covalent geometry : angle 0.62010 ( 9323) hydrogen bonds : bond 0.04904 ( 313) hydrogen bonds : angle 4.64625 ( 900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.213 Fit side-chains REVERT: A 50 ASN cc_start: 0.8683 (t0) cc_final: 0.8319 (t0) REVERT: A 301 MET cc_start: 0.8382 (mmp) cc_final: 0.7807 (mmp) REVERT: A 377 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8660 (tmm) REVERT: A 415 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: B 165 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8923 (pt0) REVERT: B 212 PHE cc_start: 0.7457 (m-10) cc_final: 0.7222 (m-10) REVERT: B 321 MET cc_start: 0.8513 (ptp) cc_final: 0.7957 (ptp) outliers start: 18 outliers final: 10 residues processed: 84 average time/residue: 0.5598 time to fit residues: 49.7484 Evaluate side-chains 81 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.082857 restraints weight = 9762.457| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.27 r_work: 0.3181 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6873 Z= 0.137 Angle : 0.554 8.919 9323 Z= 0.289 Chirality : 0.042 0.136 1016 Planarity : 0.004 0.034 1214 Dihedral : 12.407 177.375 971 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.66 % Allowed : 15.06 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.42 (0.29), residues: 847 helix: 1.54 (0.27), residues: 381 sheet: -0.24 (0.47), residues: 136 loop : -0.96 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 306 TYR 0.009 0.001 TYR B 159 PHE 0.031 0.001 PHE A 255 TRP 0.017 0.002 TRP A 21 HIS 0.002 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6873) covalent geometry : angle 0.55426 ( 9323) hydrogen bonds : bond 0.03832 ( 313) hydrogen bonds : angle 4.41260 ( 900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.295 Fit side-chains REVERT: A 50 ASN cc_start: 0.8679 (t0) cc_final: 0.8335 (t0) REVERT: A 301 MET cc_start: 0.8303 (mmp) cc_final: 0.8036 (mmp) REVERT: A 415 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: B 165 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8843 (pt0) REVERT: B 212 PHE cc_start: 0.7439 (m-10) cc_final: 0.7160 (m-10) REVERT: B 321 MET cc_start: 0.8446 (ptp) cc_final: 0.8075 (ptp) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.5332 time to fit residues: 45.2700 Evaluate side-chains 78 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 168 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.081282 restraints weight = 9941.545| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.27 r_work: 0.3150 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6873 Z= 0.214 Angle : 0.604 8.532 9323 Z= 0.313 Chirality : 0.044 0.135 1016 Planarity : 0.004 0.035 1214 Dihedral : 12.505 177.239 971 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.93 % Allowed : 14.78 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.20 (0.29), residues: 847 helix: 1.29 (0.27), residues: 382 sheet: -0.31 (0.47), residues: 136 loop : -1.00 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 306 TYR 0.012 0.001 TYR B 159 PHE 0.032 0.002 PHE A 255 TRP 0.014 0.002 TRP A 21 HIS 0.011 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 6873) covalent geometry : angle 0.60404 ( 9323) hydrogen bonds : bond 0.04431 ( 313) hydrogen bonds : angle 4.55683 ( 900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.263 Fit side-chains REVERT: A 50 ASN cc_start: 0.8715 (t0) cc_final: 0.8358 (t0) REVERT: A 301 MET cc_start: 0.8385 (mmp) cc_final: 0.7934 (mmp) REVERT: A 415 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: B 165 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8902 (pt0) REVERT: B 212 PHE cc_start: 0.7476 (m-10) cc_final: 0.7254 (m-10) REVERT: B 321 MET cc_start: 0.8531 (ptp) cc_final: 0.7986 (ptp) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.5466 time to fit residues: 48.1094 Evaluate side-chains 81 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 168 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.100180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.082507 restraints weight = 9832.767| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.27 r_work: 0.3178 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6873 Z= 0.165 Angle : 0.572 8.347 9323 Z= 0.298 Chirality : 0.043 0.133 1016 Planarity : 0.004 0.035 1214 Dihedral : 12.416 177.252 971 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.21 % Allowed : 14.50 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.33 (0.29), residues: 847 helix: 1.42 (0.27), residues: 382 sheet: -0.21 (0.47), residues: 133 loop : -0.98 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.010 0.001 TYR B 159 PHE 0.031 0.001 PHE A 255 TRP 0.016 0.002 TRP A 21 HIS 0.010 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 6873) covalent geometry : angle 0.57233 ( 9323) hydrogen bonds : bond 0.04001 ( 313) hydrogen bonds : angle 4.45138 ( 900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.264 Fit side-chains REVERT: A 50 ASN cc_start: 0.8722 (t0) cc_final: 0.8387 (t0) REVERT: A 301 MET cc_start: 0.8284 (mmp) cc_final: 0.7997 (mmp) REVERT: A 377 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8578 (tmm) REVERT: A 415 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: B 165 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8872 (pt0) REVERT: B 212 PHE cc_start: 0.7472 (m-10) cc_final: 0.7199 (m-10) REVERT: B 321 MET cc_start: 0.8492 (ptp) cc_final: 0.8115 (ptp) outliers start: 16 outliers final: 10 residues processed: 82 average time/residue: 0.5207 time to fit residues: 45.4861 Evaluate side-chains 81 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 35 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 168 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.102540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.085008 restraints weight = 9794.770| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.27 r_work: 0.3226 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6873 Z= 0.112 Angle : 0.537 8.114 9323 Z= 0.279 Chirality : 0.041 0.135 1016 Planarity : 0.004 0.035 1214 Dihedral : 12.172 176.708 971 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.80 % Allowed : 15.06 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.53 (0.30), residues: 847 helix: 1.70 (0.27), residues: 381 sheet: -0.30 (0.47), residues: 136 loop : -0.95 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 339 TYR 0.007 0.001 TYR B 159 PHE 0.031 0.001 PHE A 255 TRP 0.017 0.002 TRP A 21 HIS 0.011 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6873) covalent geometry : angle 0.53660 ( 9323) hydrogen bonds : bond 0.03377 ( 313) hydrogen bonds : angle 4.23846 ( 900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2714.68 seconds wall clock time: 47 minutes 2.70 seconds (2822.70 seconds total)