Starting phenix.real_space_refine on Sat Dec 28 07:32:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dtg_47155/12_2024/9dtg_47155.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dtg_47155/12_2024/9dtg_47155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dtg_47155/12_2024/9dtg_47155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dtg_47155/12_2024/9dtg_47155.map" model { file = "/net/cci-nas-00/data/ceres_data/9dtg_47155/12_2024/9dtg_47155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dtg_47155/12_2024/9dtg_47155.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 46 5.16 5 C 5104 2.51 5 N 1386 2.21 5 O 1533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8069 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4039 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 496} Chain: "B" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4030 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 15, 'TRANS': 495} Chain breaks: 1 Time building chain proxies: 5.66, per 1000 atoms: 0.70 Number of scatterers: 8069 At special positions: 0 Unit cell: (74.34, 98.235, 138.945, 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 46 16.00 O 1533 8.00 N 1386 7.00 C 5104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.2 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 19 sheets defined 24.5% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.723A pdb=" N GLN A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 78 through 83 removed outlier: 4.077A pdb=" N HIS A 82 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 4.074A pdb=" N GLN A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 removed outlier: 3.555A pdb=" N LEU A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.643A pdb=" N GLU A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 123 " --> pdb=" O TYR A 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 removed outlier: 4.204A pdb=" N ARG A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.554A pdb=" N THR A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.640A pdb=" N LEU A 177 " --> pdb=" O HIS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.934A pdb=" N LEU A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 185' Processing helix chain 'A' and resid 187 through 195 removed outlier: 4.205A pdb=" N ASP A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.718A pdb=" N ILE A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 removed outlier: 4.233A pdb=" N GLU A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.927A pdb=" N TRP A 460 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 461 " --> pdb=" O GLU A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 461' Processing helix chain 'B' and resid 31 through 39 removed outlier: 3.688A pdb=" N LYS B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU B 37 " --> pdb=" O GLY B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 removed outlier: 3.572A pdb=" N LEU B 63 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.652A pdb=" N PHE B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 removed outlier: 3.538A pdb=" N GLN B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 139 removed outlier: 3.656A pdb=" N LEU B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 167 through 172 removed outlier: 4.159A pdb=" N THR B 172 " --> pdb=" O HIS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 180 removed outlier: 4.329A pdb=" N ASN B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.965A pdb=" N LEU B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 185' Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.522A pdb=" N THR B 192 " --> pdb=" O HIS B 188 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.746A pdb=" N ALA B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 209 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TRP B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.880A pdb=" N ALA B 222 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE B 223 " --> pdb=" O ARG B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 223' Processing helix chain 'B' and resid 326 through 330 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 200 removed outlier: 6.291A pdb=" N VAL A 199 " --> pdb=" O ILE A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 271 removed outlier: 5.241A pdb=" N SER A 256 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLN A 270 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA A 254 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 243 " --> pdb=" O VAL A 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.892A pdb=" N VAL A 290 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 286 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.892A pdb=" N VAL A 290 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 291 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.555A pdb=" N VAL A 324 " --> pdb=" O TYR A 333 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 326 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA A 331 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 351 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 374 Processing sheet with id=AA9, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AB1, first strand: chain 'A' and resid 424 through 428 Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 472 removed outlier: 3.744A pdb=" N CYS A 472 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.536A pdb=" N VAL B 47 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 200 removed outlier: 5.666A pdb=" N VAL B 199 " --> pdb=" O ILE B 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 270 through 272 removed outlier: 4.098A pdb=" N ASN B 271 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 257 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 515 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 277 through 283 removed outlier: 3.579A pdb=" N GLY B 291 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG B 297 " --> pdb=" O GLY B 291 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AB8, first strand: chain 'B' and resid 372 through 376 removed outlier: 3.887A pdb=" N CYS B 402 " --> pdb=" O HIS B 411 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS B 411 " --> pdb=" O CYS B 402 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 424 through 428 removed outlier: 3.607A pdb=" N ALA B 426 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 433 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 432 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 467 through 472 removed outlier: 3.643A pdb=" N CYS B 472 " --> pdb=" O SER B 475 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 414 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: 2.05 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2441 1.33 - 1.45: 1225 1.45 - 1.57: 4517 1.57 - 1.69: 1 1.69 - 1.81: 60 Bond restraints: 8244 Sorted by residual: bond pdb=" N SER A 325 " pdb=" CA SER A 325 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.26e-02 6.30e+03 1.06e+01 bond pdb=" N VAL A 326 " pdb=" CA VAL A 326 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.23e-02 6.61e+03 9.96e+00 bond pdb=" N LYS A 329 " pdb=" CA LYS A 329 " ideal model delta sigma weight residual 1.462 1.499 -0.037 1.32e-02 5.74e+03 7.76e+00 bond pdb=" N LYS B 329 " pdb=" CA LYS B 329 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.19e-02 7.06e+03 6.80e+00 bond pdb=" CA SER A 325 " pdb=" CB SER A 325 " ideal model delta sigma weight residual 1.534 1.489 0.044 1.72e-02 3.38e+03 6.66e+00 ... (remaining 8239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 11013 2.17 - 4.33: 151 4.33 - 6.50: 20 6.50 - 8.66: 5 8.66 - 10.83: 3 Bond angle restraints: 11192 Sorted by residual: angle pdb=" N ASP B 12 " pdb=" CA ASP B 12 " pdb=" C ASP B 12 " ideal model delta sigma weight residual 112.54 104.48 8.06 1.51e+00 4.39e-01 2.85e+01 angle pdb=" N GLY A 328 " pdb=" CA GLY A 328 " pdb=" C GLY A 328 " ideal model delta sigma weight residual 115.73 107.56 8.17 1.59e+00 3.96e-01 2.64e+01 angle pdb=" C LYS A 429 " pdb=" CA LYS A 429 " pdb=" CB LYS A 429 " ideal model delta sigma weight residual 116.54 110.68 5.86 1.15e+00 7.56e-01 2.59e+01 angle pdb=" N MET A 11 " pdb=" CA MET A 11 " pdb=" C MET A 11 " ideal model delta sigma weight residual 113.23 107.71 5.52 1.24e+00 6.50e-01 1.98e+01 angle pdb=" C ALA A 9 " pdb=" N SER A 10 " pdb=" CA SER A 10 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 ... (remaining 11187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4391 17.97 - 35.94: 414 35.94 - 53.91: 90 53.91 - 71.88: 12 71.88 - 89.86: 2 Dihedral angle restraints: 4909 sinusoidal: 1919 harmonic: 2990 Sorted by residual: dihedral pdb=" CA TYR B 104 " pdb=" C TYR B 104 " pdb=" N HIS B 105 " pdb=" CA HIS B 105 " ideal model delta harmonic sigma weight residual -180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA MET B 11 " pdb=" C MET B 11 " pdb=" N ASP B 12 " pdb=" CA ASP B 12 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA VAL B 17 " pdb=" C VAL B 17 " pdb=" N ASN B 18 " pdb=" CA ASN B 18 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 4906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1117 0.063 - 0.126: 136 0.126 - 0.188: 12 0.188 - 0.251: 1 0.251 - 0.314: 1 Chirality restraints: 1267 Sorted by residual: chirality pdb=" CB VAL A 326 " pdb=" CA VAL A 326 " pdb=" CG1 VAL A 326 " pdb=" CG2 VAL A 326 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA VAL B 326 " pdb=" N VAL B 326 " pdb=" C VAL B 326 " pdb=" CB VAL B 326 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL A 326 " pdb=" N VAL A 326 " pdb=" C VAL A 326 " pdb=" CB VAL A 326 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1264 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 294 " -0.033 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 295 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 20 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C THR B 20 " 0.024 2.00e-02 2.50e+03 pdb=" O THR B 20 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE B 21 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 500 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" C VAL A 500 " 0.022 2.00e-02 2.50e+03 pdb=" O VAL A 500 " -0.008 2.00e-02 2.50e+03 pdb=" N THR A 501 " -0.007 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 565 2.74 - 3.28: 7605 3.28 - 3.82: 11608 3.82 - 4.36: 13755 4.36 - 4.90: 23817 Nonbonded interactions: 57350 Sorted by model distance: nonbonded pdb=" O SER B 196 " pdb=" OG SER B 196 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR A 339 " pdb=" OG1 THR A 343 " model vdw 2.221 3.040 nonbonded pdb=" O THR A 490 " pdb=" OG1 THR A 490 " model vdw 2.238 3.040 nonbonded pdb=" OG SER B 247 " pdb=" OG1 THR B 511 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASN A 271 " pdb=" NE1 TRP A 308 " model vdw 2.282 3.120 ... (remaining 57345 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 216 or resid 218 through 518)) selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.990 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.270 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 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 0.046 8244 Z= 0.199 Angle : 0.651 10.829 11192 Z= 0.368 Chirality : 0.044 0.314 1267 Planarity : 0.003 0.048 1438 Dihedral : 14.386 89.856 2972 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.24 % Favored : 90.56 % Rotamer: Outliers : 0.79 % Allowed : 22.16 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.24), residues: 1017 helix: -3.59 (0.26), residues: 224 sheet: -2.59 (0.35), residues: 218 loop : -2.20 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 310 HIS 0.002 0.001 HIS B 105 PHE 0.008 0.001 PHE B 16 TYR 0.016 0.001 TYR A 241 ARG 0.005 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.988 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 0.2258 time to fit residues: 25.6334 Evaluate side-chains 78 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 105 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8244 Z= 0.271 Angle : 0.584 8.263 11192 Z= 0.308 Chirality : 0.045 0.148 1267 Planarity : 0.004 0.030 1438 Dihedral : 4.934 43.206 1112 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.13 % Favored : 89.77 % Rotamer: Outliers : 5.06 % Allowed : 19.01 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.23), residues: 1017 helix: -3.28 (0.25), residues: 244 sheet: -2.69 (0.34), residues: 214 loop : -2.49 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 299 HIS 0.004 0.001 HIS A 258 PHE 0.014 0.002 PHE A 96 TYR 0.019 0.002 TYR B 19 ARG 0.003 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 93 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8480 (tppt) cc_final: 0.7892 (ttmt) REVERT: B 295 PRO cc_start: 0.7735 (Cg_endo) cc_final: 0.7530 (Cg_exo) outliers start: 45 outliers final: 23 residues processed: 128 average time/residue: 0.1937 time to fit residues: 34.4722 Evaluate side-chains 104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 ASN ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8244 Z= 0.385 Angle : 0.646 8.705 11192 Z= 0.337 Chirality : 0.047 0.158 1267 Planarity : 0.004 0.035 1438 Dihedral : 5.376 50.851 1109 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.11 % Favored : 88.79 % Rotamer: Outliers : 5.40 % Allowed : 19.35 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.23), residues: 1017 helix: -3.28 (0.25), residues: 240 sheet: -2.77 (0.33), residues: 225 loop : -2.51 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 299 HIS 0.005 0.001 HIS A 173 PHE 0.015 0.002 PHE B 96 TYR 0.027 0.002 TYR B 19 ARG 0.003 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8588 (tppt) cc_final: 0.8029 (ttmt) REVERT: B 19 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6778 (m-80) REVERT: B 295 PRO cc_start: 0.7694 (Cg_endo) cc_final: 0.7378 (Cg_exo) outliers start: 48 outliers final: 29 residues processed: 130 average time/residue: 0.1764 time to fit residues: 33.1393 Evaluate side-chains 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 447 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8244 Z= 0.211 Angle : 0.554 11.221 11192 Z= 0.288 Chirality : 0.044 0.223 1267 Planarity : 0.003 0.030 1438 Dihedral : 5.045 56.304 1109 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.13 % Favored : 89.77 % Rotamer: Outliers : 4.39 % Allowed : 20.70 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.23), residues: 1017 helix: -3.04 (0.27), residues: 240 sheet: -2.74 (0.33), residues: 220 loop : -2.49 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 460 HIS 0.002 0.001 HIS A 321 PHE 0.011 0.001 PHE B 96 TYR 0.015 0.002 TYR B 119 ARG 0.002 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8529 (tppt) cc_final: 0.8014 (ttmt) REVERT: A 231 LEU cc_start: 0.8307 (tt) cc_final: 0.7944 (tt) REVERT: A 299 TRP cc_start: 0.8976 (m-90) cc_final: 0.8750 (m-10) REVERT: B 19 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: B 295 PRO cc_start: 0.7581 (Cg_endo) cc_final: 0.7313 (Cg_exo) REVERT: B 344 LEU cc_start: 0.1810 (OUTLIER) cc_final: 0.1194 (mt) outliers start: 39 outliers final: 27 residues processed: 119 average time/residue: 0.2007 time to fit residues: 33.0162 Evaluate side-chains 109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 0.0870 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8244 Z= 0.225 Angle : 0.549 9.253 11192 Z= 0.286 Chirality : 0.044 0.163 1267 Planarity : 0.003 0.029 1438 Dihedral : 5.052 59.742 1109 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.62 % Favored : 89.28 % Rotamer: Outliers : 5.62 % Allowed : 20.58 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.23), residues: 1017 helix: -2.90 (0.28), residues: 238 sheet: -2.78 (0.32), residues: 225 loop : -2.46 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 310 HIS 0.002 0.001 HIS A 173 PHE 0.012 0.001 PHE B 96 TYR 0.016 0.002 TYR B 119 ARG 0.002 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 85 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8519 (tppt) cc_final: 0.8037 (ttmt) REVERT: A 195 ILE cc_start: 0.8871 (mm) cc_final: 0.8661 (mt) REVERT: A 299 TRP cc_start: 0.8964 (m-90) cc_final: 0.8751 (m-10) REVERT: B 19 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: B 114 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8146 (pp20) REVERT: B 295 PRO cc_start: 0.7597 (Cg_endo) cc_final: 0.7319 (Cg_exo) REVERT: B 344 LEU cc_start: 0.1678 (OUTLIER) cc_final: 0.1350 (mt) outliers start: 50 outliers final: 33 residues processed: 125 average time/residue: 0.1908 time to fit residues: 33.4214 Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 51 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8244 Z= 0.164 Angle : 0.531 11.679 11192 Z= 0.271 Chirality : 0.042 0.164 1267 Planarity : 0.003 0.027 1438 Dihedral : 4.758 56.020 1109 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.13 % Favored : 89.77 % Rotamer: Outliers : 4.39 % Allowed : 20.92 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.23), residues: 1017 helix: -2.69 (0.29), residues: 239 sheet: -2.62 (0.34), residues: 209 loop : -2.39 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 310 HIS 0.002 0.000 HIS B 59 PHE 0.009 0.001 PHE B 96 TYR 0.013 0.001 TYR B 119 ARG 0.002 0.000 ARG A 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8465 (tppt) cc_final: 0.8020 (ttmt) REVERT: A 231 LEU cc_start: 0.8145 (tt) cc_final: 0.7766 (tt) REVERT: A 299 TRP cc_start: 0.8921 (m-90) cc_final: 0.8685 (m-10) REVERT: B 19 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6244 (m-80) REVERT: B 114 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8160 (pp20) REVERT: B 295 PRO cc_start: 0.7455 (Cg_endo) cc_final: 0.7232 (Cg_exo) REVERT: B 344 LEU cc_start: 0.1919 (OUTLIER) cc_final: 0.1403 (mt) outliers start: 39 outliers final: 25 residues processed: 114 average time/residue: 0.1678 time to fit residues: 28.0446 Evaluate side-chains 104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8244 Z= 0.238 Angle : 0.563 10.506 11192 Z= 0.287 Chirality : 0.044 0.177 1267 Planarity : 0.003 0.029 1438 Dihedral : 4.922 55.301 1109 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.01 % Favored : 88.89 % Rotamer: Outliers : 5.62 % Allowed : 19.91 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.23), residues: 1017 helix: -2.70 (0.29), residues: 240 sheet: -2.61 (0.33), residues: 214 loop : -2.40 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.003 0.001 HIS B 59 PHE 0.013 0.001 PHE B 16 TYR 0.016 0.002 TYR B 119 ARG 0.002 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 84 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8548 (tppt) cc_final: 0.8123 (ttmt) REVERT: A 299 TRP cc_start: 0.8973 (m-90) cc_final: 0.8719 (m-10) REVERT: B 19 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: B 114 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8140 (pp20) REVERT: B 295 PRO cc_start: 0.7586 (Cg_endo) cc_final: 0.7294 (Cg_exo) REVERT: B 344 LEU cc_start: 0.2091 (OUTLIER) cc_final: 0.1665 (mt) outliers start: 50 outliers final: 33 residues processed: 125 average time/residue: 0.1856 time to fit residues: 33.1590 Evaluate side-chains 117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8244 Z= 0.203 Angle : 0.552 12.750 11192 Z= 0.280 Chirality : 0.044 0.180 1267 Planarity : 0.003 0.028 1438 Dihedral : 4.818 52.425 1109 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.11 % Favored : 88.79 % Rotamer: Outliers : 4.61 % Allowed : 21.48 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.23), residues: 1017 helix: -2.63 (0.29), residues: 239 sheet: -2.62 (0.33), residues: 214 loop : -2.37 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 310 HIS 0.003 0.001 HIS B 59 PHE 0.011 0.001 PHE B 16 TYR 0.016 0.002 TYR B 119 ARG 0.002 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8544 (tppt) cc_final: 0.8132 (ttmt) REVERT: A 299 TRP cc_start: 0.8931 (m-90) cc_final: 0.8697 (m-10) REVERT: B 19 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6419 (m-80) REVERT: B 114 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8129 (pp20) REVERT: B 295 PRO cc_start: 0.7491 (Cg_endo) cc_final: 0.7206 (Cg_exo) REVERT: B 344 LEU cc_start: 0.2271 (OUTLIER) cc_final: 0.1887 (mt) outliers start: 41 outliers final: 32 residues processed: 116 average time/residue: 0.1765 time to fit residues: 29.3786 Evaluate side-chains 114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.0770 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8244 Z= 0.208 Angle : 0.560 12.968 11192 Z= 0.285 Chirality : 0.044 0.191 1267 Planarity : 0.003 0.028 1438 Dihedral : 4.827 51.578 1109 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.62 % Favored : 89.28 % Rotamer: Outliers : 4.95 % Allowed : 21.37 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.24), residues: 1017 helix: -2.61 (0.29), residues: 239 sheet: -2.62 (0.33), residues: 221 loop : -2.27 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.003 0.001 HIS B 59 PHE 0.011 0.001 PHE B 96 TYR 0.016 0.002 TYR B 119 ARG 0.005 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8601 (tppt) cc_final: 0.8174 (ttmt) REVERT: B 19 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: B 114 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: B 295 PRO cc_start: 0.7574 (Cg_endo) cc_final: 0.7333 (Cg_exo) REVERT: B 318 ARG cc_start: 0.6259 (mtt180) cc_final: 0.5976 (mtt180) REVERT: B 344 LEU cc_start: 0.2399 (OUTLIER) cc_final: 0.2059 (mt) outliers start: 44 outliers final: 35 residues processed: 118 average time/residue: 0.1931 time to fit residues: 32.7358 Evaluate side-chains 116 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.0170 chunk 93 optimal weight: 0.3980 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8244 Z= 0.170 Angle : 0.553 12.970 11192 Z= 0.279 Chirality : 0.043 0.192 1267 Planarity : 0.003 0.028 1438 Dihedral : 4.654 49.579 1109 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.42 % Favored : 89.48 % Rotamer: Outliers : 4.27 % Allowed : 22.27 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.24), residues: 1017 helix: -2.52 (0.30), residues: 240 sheet: -2.62 (0.33), residues: 223 loop : -2.20 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 299 HIS 0.004 0.000 HIS B 59 PHE 0.010 0.001 PHE B 96 TYR 0.014 0.001 TYR B 119 ARG 0.003 0.000 ARG B 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 0.947 Fit side-chains REVERT: A 22 LYS cc_start: 0.8577 (tppt) cc_final: 0.8172 (ttmt) REVERT: B 19 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: B 114 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8131 (pp20) REVERT: B 295 PRO cc_start: 0.7440 (Cg_endo) cc_final: 0.7229 (Cg_exo) REVERT: B 318 ARG cc_start: 0.6245 (mtt180) cc_final: 0.5948 (mtt180) REVERT: B 344 LEU cc_start: 0.2408 (OUTLIER) cc_final: 0.2117 (mt) outliers start: 38 outliers final: 34 residues processed: 109 average time/residue: 0.1775 time to fit residues: 27.7651 Evaluate side-chains 112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain B residue 18 ASN Chi-restraints excluded: chain B residue 19 TYR Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 0.0010 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 HIS ** 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 = 0.3893 r_free = 0.3893 target = 0.172025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.158216 restraints weight = 8583.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.153215 restraints weight = 14413.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151901 restraints weight = 20236.066| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8244 Z= 0.216 Angle : 0.569 12.885 11192 Z= 0.289 Chirality : 0.044 0.211 1267 Planarity : 0.003 0.028 1438 Dihedral : 4.786 49.689 1109 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.72 % Favored : 89.18 % Rotamer: Outliers : 4.39 % Allowed : 22.50 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.24), residues: 1017 helix: -2.56 (0.29), residues: 240 sheet: -2.63 (0.33), residues: 223 loop : -2.20 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 299 HIS 0.004 0.001 HIS B 59 PHE 0.011 0.001 PHE B 96 TYR 0.015 0.002 TYR B 119 ARG 0.004 0.000 ARG A 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.33 seconds wall clock time: 35 minutes 20.42 seconds (2120.42 seconds total)