Starting phenix.real_space_refine on Fri May 16 11:06:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptw_17879/05_2025/8ptw_17879.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptw_17879/05_2025/8ptw_17879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ptw_17879/05_2025/8ptw_17879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptw_17879/05_2025/8ptw_17879.map" model { file = "/net/cci-nas-00/data/ceres_data/8ptw_17879/05_2025/8ptw_17879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptw_17879/05_2025/8ptw_17879.cif" } resolution = 2.91 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= 0.005 sd= 0.085 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 64 5.16 5 C 9064 2.51 5 N 2436 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14242 Number of models: 1 Model: "" Number of chains: 4 Chain: "CT" Number of atoms: 2936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2936 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 367} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "CV" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4185 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 499} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "CU" Number of atoms: 2936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2936 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 367} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "CW" Number of atoms: 4185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4185 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 499} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 8.46, per 1000 atoms: 0.59 Number of scatterers: 14242 At special positions: 0 Unit cell: (128.535, 113.905, 106.59, 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 64 16.00 O 2678 8.00 N 2436 7.00 C 9064 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: 3.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 18 sheets defined 49.2% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'CT' and resid 153 through 158 Processing helix chain 'CT' and resid 369 through 377 Processing helix chain 'CT' and resid 381 through 393 Processing helix chain 'CV' and resid 4 through 17 removed outlier: 3.529A pdb=" N ARGCV 8 " --> pdb=" O PROCV 4 " (cutoff:3.500A) Processing helix chain 'CV' and resid 21 through 36 Proline residue: CV 27 - end of helix Processing helix chain 'CV' and resid 36 through 42 removed outlier: 4.070A pdb=" N LEUCV 40 " --> pdb=" O CYSCV 36 " (cutoff:3.500A) Processing helix chain 'CV' and resid 53 through 72 Processing helix chain 'CV' and resid 74 through 93 removed outlier: 4.153A pdb=" N GLYCV 93 " --> pdb=" O ILECV 89 " (cutoff:3.500A) Processing helix chain 'CV' and resid 93 through 98 Processing helix chain 'CV' and resid 100 through 113 Processing helix chain 'CV' and resid 116 through 135 Processing helix chain 'CV' and resid 137 through 144 Processing helix chain 'CV' and resid 144 through 161 Proline residue: CV 150 - end of helix Processing helix chain 'CV' and resid 172 through 190 removed outlier: 3.554A pdb=" N LYSCV 185 " --> pdb=" O TRPCV 181 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VALCV 188 " --> pdb=" O SERCV 184 " (cutoff:3.500A) Processing helix chain 'CV' and resid 190 through 195 Processing helix chain 'CV' and resid 197 through 206 Processing helix chain 'CV' and resid 207 through 209 No H-bonds generated for 'chain 'CV' and resid 207 through 209' Processing helix chain 'CV' and resid 212 through 216 Processing helix chain 'CV' and resid 220 through 234 Processing helix chain 'CV' and resid 235 through 241 Proline residue: CV 239 - end of helix Processing helix chain 'CV' and resid 242 through 266 removed outlier: 3.648A pdb=" N GLNCV 264 " --> pdb=" O THRCV 260 " (cutoff:3.500A) Processing helix chain 'CV' and resid 305 through 326 removed outlier: 3.640A pdb=" N PHECV 324 " --> pdb=" O LEUCV 320 " (cutoff:3.500A) Processing helix chain 'CV' and resid 336 through 349 removed outlier: 3.970A pdb=" N VALCV 349 " --> pdb=" O ARGCV 345 " (cutoff:3.500A) Processing helix chain 'CV' and resid 356 through 360 removed outlier: 3.584A pdb=" N ILECV 360 " --> pdb=" O GLUCV 357 " (cutoff:3.500A) Processing helix chain 'CV' and resid 367 through 397 Proline residue: CV 379 - end of helix Processing helix chain 'CV' and resid 398 through 402 Proline residue: CV 402 - end of helix Processing helix chain 'CV' and resid 403 through 418 Processing helix chain 'CV' and resid 421 through 440 removed outlier: 3.573A pdb=" N GLUCV 434 " --> pdb=" O ILECV 430 " (cutoff:3.500A) Processing helix chain 'CV' and resid 444 through 467 Proline residue: CV 453 - end of helix Processing helix chain 'CV' and resid 515 through 531 Proline residue: CV 526 - end of helix removed outlier: 3.994A pdb=" N PHECV 529 " --> pdb=" O LEUCV 525 " (cutoff:3.500A) Processing helix chain 'CV' and resid 538 through 553 Processing helix chain 'CV' and resid 554 through 564 Processing helix chain 'CV' and resid 577 through 585 Processing helix chain 'CV' and resid 588 through 595 Processing helix chain 'CU' and resid 153 through 158 Processing helix chain 'CU' and resid 369 through 377 Processing helix chain 'CU' and resid 381 through 393 Processing helix chain 'CW' and resid 4 through 17 removed outlier: 3.618A pdb=" N ARGCW 8 " --> pdb=" O PROCW 4 " (cutoff:3.500A) Processing helix chain 'CW' and resid 21 through 36 Proline residue: CW 27 - end of helix Processing helix chain 'CW' and resid 36 through 42 removed outlier: 4.108A pdb=" N LEUCW 40 " --> pdb=" O CYSCW 36 " (cutoff:3.500A) Processing helix chain 'CW' and resid 53 through 72 Processing helix chain 'CW' and resid 74 through 93 removed outlier: 4.121A pdb=" N GLYCW 93 " --> pdb=" O ILECW 89 " (cutoff:3.500A) Processing helix chain 'CW' and resid 93 through 99 removed outlier: 3.639A pdb=" N SERCW 99 " --> pdb=" O GLUCW 95 " (cutoff:3.500A) Processing helix chain 'CW' and resid 100 through 113 Processing helix chain 'CW' and resid 116 through 135 Processing helix chain 'CW' and resid 137 through 144 Processing helix chain 'CW' and resid 144 through 161 Proline residue: CW 150 - end of helix Processing helix chain 'CW' and resid 172 through 190 removed outlier: 3.555A pdb=" N LYSCW 185 " --> pdb=" O TRPCW 181 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VALCW 188 " --> pdb=" O SERCW 184 " (cutoff:3.500A) Processing helix chain 'CW' and resid 190 through 195 Processing helix chain 'CW' and resid 197 through 206 Processing helix chain 'CW' and resid 207 through 209 No H-bonds generated for 'chain 'CW' and resid 207 through 209' Processing helix chain 'CW' and resid 212 through 216 Processing helix chain 'CW' and resid 220 through 234 Processing helix chain 'CW' and resid 235 through 241 Proline residue: CW 239 - end of helix Processing helix chain 'CW' and resid 242 through 266 removed outlier: 3.652A pdb=" N GLNCW 264 " --> pdb=" O THRCW 260 " (cutoff:3.500A) Processing helix chain 'CW' and resid 305 through 326 removed outlier: 3.642A pdb=" N PHECW 324 " --> pdb=" O LEUCW 320 " (cutoff:3.500A) Processing helix chain 'CW' and resid 336 through 349 removed outlier: 3.978A pdb=" N VALCW 349 " --> pdb=" O ARGCW 345 " (cutoff:3.500A) Processing helix chain 'CW' and resid 356 through 360 removed outlier: 3.619A pdb=" N ILECW 360 " --> pdb=" O GLUCW 357 " (cutoff:3.500A) Processing helix chain 'CW' and resid 367 through 397 Proline residue: CW 379 - end of helix Processing helix chain 'CW' and resid 398 through 402 Proline residue: CW 402 - end of helix Processing helix chain 'CW' and resid 403 through 418 Processing helix chain 'CW' and resid 421 through 440 removed outlier: 3.566A pdb=" N GLUCW 434 " --> pdb=" O ILECW 430 " (cutoff:3.500A) Processing helix chain 'CW' and resid 444 through 467 Proline residue: CW 453 - end of helix Processing helix chain 'CW' and resid 515 through 531 Proline residue: CW 526 - end of helix removed outlier: 3.989A pdb=" N PHECW 529 " --> pdb=" O LEUCW 525 " (cutoff:3.500A) Processing helix chain 'CW' and resid 533 through 537 Processing helix chain 'CW' and resid 538 through 553 Processing helix chain 'CW' and resid 554 through 564 Processing helix chain 'CW' and resid 577 through 585 Processing helix chain 'CW' and resid 588 through 595 Processing sheet with id=AA1, first strand: chain 'CT' and resid 37 through 43 removed outlier: 5.994A pdb=" N VALCT 38 " --> pdb=" O THRCT 31 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THRCT 31 " --> pdb=" O VALCT 38 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SERCT 40 " --> pdb=" O CYSCT 29 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLYCT 26 " --> pdb=" O ILECT 10 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLUCT 4 " --> pdb=" O LEUCT 32 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLUCT 5 " --> pdb=" O VALCT 331 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYSCT 11 " --> pdb=" O VALCT 325 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VALCT 325 " --> pdb=" O CYSCT 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'CT' and resid 52 through 54 removed outlier: 5.939A pdb=" N VALCT 69 " --> pdb=" O PHECT 82 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHECT 82 " --> pdb=" O VALCT 69 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VALCT 71 " --> pdb=" O GLUCT 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'CT' and resid 89 through 95 removed outlier: 3.659A pdb=" N CYSCT 91 " --> pdb=" O GLYCT 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'CT' and resid 129 through 134 Processing sheet with id=AA5, first strand: chain 'CT' and resid 178 through 183 removed outlier: 3.553A pdb=" N ALACT 180 " --> pdb=" O ALACT 197 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SERCT 202 " --> pdb=" O SERCT 198 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYSCT 203 " --> pdb=" O THRCT 216 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THRCT 216 " --> pdb=" O CYSCT 203 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILECT 205 " --> pdb=" O LEUCT 214 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N VALCT 267 " --> pdb=" O LEUCT 214 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THRCT 216 " --> pdb=" O VALCT 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'CT' and resid 223 through 228 removed outlier: 4.093A pdb=" N CYSCT 225 " --> pdb=" O SERCT 238 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SERCT 243 " --> pdb=" O CYSCT 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'CT' and resid 285 through 288 removed outlier: 6.743A pdb=" N ILECT 304 " --> pdb=" O LEUCT 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'CT' and resid 340 through 341 Processing sheet with id=AA9, first strand: chain 'CV' and resid 291 through 292 Processing sheet with id=AB1, first strand: chain 'CU' and resid 37 through 43 removed outlier: 6.067A pdb=" N VALCU 38 " --> pdb=" O THRCU 31 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THRCU 31 " --> pdb=" O VALCU 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SERCU 40 " --> pdb=" O CYSCU 29 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLYCU 26 " --> pdb=" O ILECU 10 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLUCU 4 " --> pdb=" O LEUCU 32 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLUCU 5 " --> pdb=" O PHECU 330 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHECU 330 " --> pdb=" O GLUCU 5 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VALCU 7 " --> pdb=" O LEUCU 328 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEUCU 328 " --> pdb=" O VALCU 7 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALACU 9 " --> pdb=" O THRCU 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'CU' and resid 52 through 54 removed outlier: 5.938A pdb=" N VALCU 69 " --> pdb=" O PHECU 82 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHECU 82 " --> pdb=" O VALCU 69 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VALCU 71 " --> pdb=" O GLUCU 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'CU' and resid 89 through 95 removed outlier: 3.672A pdb=" N CYSCU 91 " --> pdb=" O GLYCU 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'CU' and resid 129 through 134 Processing sheet with id=AB5, first strand: chain 'CU' and resid 178 through 183 removed outlier: 3.506A pdb=" N ALACU 180 " --> pdb=" O ALACU 197 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SERCU 202 " --> pdb=" O SERCU 198 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYSCU 203 " --> pdb=" O THRCU 216 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THRCU 216 " --> pdb=" O CYSCU 203 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILECU 205 " --> pdb=" O LEUCU 214 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N VALCU 267 " --> pdb=" O LEUCU 214 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THRCU 216 " --> pdb=" O VALCU 267 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'CU' and resid 223 through 228 removed outlier: 4.054A pdb=" N CYSCU 225 " --> pdb=" O SERCU 238 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SERCU 243 " --> pdb=" O CYSCU 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'CU' and resid 285 through 288 removed outlier: 3.527A pdb=" N CYSCU 285 " --> pdb=" O GLYCU 298 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILECU 304 " --> pdb=" O LEUCU 318 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'CU' and resid 340 through 341 Processing sheet with id=AB9, first strand: chain 'CW' and resid 291 through 292 763 hydrogen bonds defined for protein. 2193 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: 5.19 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4628 1.34 - 1.46: 2555 1.46 - 1.58: 7296 1.58 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 14568 Sorted by residual: bond pdb=" C THRCW 146 " pdb=" N PROCW 147 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.20e-02 6.94e+03 9.01e+00 bond pdb=" C THRCV 146 " pdb=" N PROCV 147 " ideal model delta sigma weight residual 1.336 1.371 -0.035 1.20e-02 6.94e+03 8.71e+00 bond pdb=" CA ARGCV 570 " pdb=" C ARGCV 570 " ideal model delta sigma weight residual 1.522 1.560 -0.038 1.37e-02 5.33e+03 7.73e+00 bond pdb=" N PROCW 301 " pdb=" CA PROCW 301 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.31e-02 5.83e+03 3.73e+00 bond pdb=" N PROCV 301 " pdb=" CA PROCV 301 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.31e-02 5.83e+03 3.66e+00 ... (remaining 14563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 19287 1.97 - 3.93: 557 3.93 - 5.90: 50 5.90 - 7.86: 20 7.86 - 9.83: 8 Bond angle restraints: 19922 Sorted by residual: angle pdb=" CA PROCW 168 " pdb=" N PROCW 168 " pdb=" CD PROCW 168 " ideal model delta sigma weight residual 112.00 102.17 9.83 1.40e+00 5.10e-01 4.93e+01 angle pdb=" CA GLNCU 277 " pdb=" CB GLNCU 277 " pdb=" CG GLNCU 277 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.66e+01 angle pdb=" C VALCT 49 " pdb=" N ASNCT 50 " pdb=" CA ASNCT 50 " ideal model delta sigma weight residual 123.47 128.77 -5.30 1.53e+00 4.27e-01 1.20e+01 angle pdb=" C VALCU 49 " pdb=" N ASNCU 50 " pdb=" CA ASNCU 50 " ideal model delta sigma weight residual 123.47 128.72 -5.25 1.53e+00 4.27e-01 1.18e+01 angle pdb=" C LEUCV 451 " pdb=" N ILECV 452 " pdb=" CA ILECV 452 " ideal model delta sigma weight residual 120.43 123.59 -3.16 9.60e-01 1.09e+00 1.08e+01 ... (remaining 19917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 8138 15.15 - 30.29: 591 30.29 - 45.44: 99 45.44 - 60.59: 18 60.59 - 75.73: 12 Dihedral angle restraints: 8858 sinusoidal: 3374 harmonic: 5484 Sorted by residual: dihedral pdb=" CA GLUCT 158 " pdb=" C GLUCT 158 " pdb=" N LEUCT 159 " pdb=" CA LEUCT 159 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA TRPCU 206 " pdb=" C TRPCU 206 " pdb=" N ASNCU 207 " pdb=" CA ASNCU 207 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TRPCT 206 " pdb=" C TRPCT 206 " pdb=" N ASNCT 207 " pdb=" CA ASNCT 207 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 8855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1934 0.055 - 0.111: 361 0.111 - 0.166: 97 0.166 - 0.221: 0 0.221 - 0.277: 2 Chirality restraints: 2394 Sorted by residual: chirality pdb=" CB ILECU 95 " pdb=" CA ILECU 95 " pdb=" CG1 ILECU 95 " pdb=" CG2 ILECU 95 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB ILECT 95 " pdb=" CA ILECT 95 " pdb=" CG1 ILECT 95 " pdb=" CG2 ILECT 95 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA CYSCW 26 " pdb=" N CYSCW 26 " pdb=" C CYSCW 26 " pdb=" CB CYSCW 26 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 2391 not shown) Planarity restraints: 2544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARGCW 167 " -0.068 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PROCW 168 " 0.166 5.00e-02 4.00e+02 pdb=" CA PROCW 168 " -0.045 5.00e-02 4.00e+02 pdb=" CD PROCW 168 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THRCT 135 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PROCT 136 " -0.118 5.00e-02 4.00e+02 pdb=" CA PROCT 136 " 0.035 5.00e-02 4.00e+02 pdb=" CD PROCT 136 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THRCU 135 " -0.043 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PROCU 136 " 0.111 5.00e-02 4.00e+02 pdb=" CA PROCU 136 " -0.033 5.00e-02 4.00e+02 pdb=" CD PROCU 136 " -0.036 5.00e-02 4.00e+02 ... (remaining 2541 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4032 2.82 - 3.34: 13389 3.34 - 3.86: 23996 3.86 - 4.38: 28059 4.38 - 4.90: 48563 Nonbonded interactions: 118039 Sorted by model distance: nonbonded pdb=" OG SERCT 130 " pdb=" O ILECT 178 " model vdw 2.299 3.040 nonbonded pdb=" OG SERCU 130 " pdb=" O ILECU 178 " model vdw 2.302 3.040 nonbonded pdb=" OE1 GLNCV 555 " pdb=" OG SERCV 590 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THRCT 31 " pdb=" OG SERCT 37 " model vdw 2.328 3.040 nonbonded pdb=" OH TYRCV 429 " pdb=" OG SERCV 457 " model vdw 2.333 3.040 ... (remaining 118034 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: 0.03 Found NCS groups: ncs_group { reference = chain 'CT' selection = chain 'CU' } ncs_group { reference = chain 'CV' selection = chain 'CW' } 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.070 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.004 0.086 14568 Z= 0.206 Angle : 0.780 9.826 19922 Z= 0.439 Chirality : 0.047 0.277 2394 Planarity : 0.008 0.096 2544 Dihedral : 11.313 75.732 5290 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.35 (0.18), residues: 1862 helix: 0.79 (0.17), residues: 824 sheet: 0.31 (0.30), residues: 278 loop : -0.29 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPCT 206 HIS 0.006 0.001 HISCV 383 PHE 0.015 0.002 PHECT 6 TYR 0.020 0.002 TYRCU 245 ARG 0.005 0.000 ARGCU 353 Details of bonding type rmsd hydrogen bonds : bond 0.15356 ( 763) hydrogen bonds : angle 5.86497 ( 2193) covalent geometry : bond 0.00429 (14568) covalent geometry : angle 0.77991 (19922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.506 Fit side-chains REVERT: CU 303 GLN cc_start: 0.8411 (mp10) cc_final: 0.8127 (mp10) REVERT: CU 307 TRP cc_start: 0.7970 (m100) cc_final: 0.7768 (m100) REVERT: CU 320 ASN cc_start: 0.8622 (t0) cc_final: 0.8338 (t0) REVERT: CW 445 LYS cc_start: 0.7486 (ttmm) cc_final: 0.7175 (tppt) outliers start: 0 outliers final: 2 residues processed: 183 average time/residue: 1.2509 time to fit residues: 251.5057 Evaluate side-chains 121 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CV residue 350 ILE Chi-restraints excluded: chain CW residue 350 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 0.0470 chunk 56 optimal weight: 0.0570 chunk 88 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CT 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 64 HIS ** CT 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CV 31 ASN CV 216 ASN ** CU 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CW 31 ASN CW 216 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116231 restraints weight = 21799.789| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.38 r_work: 0.3341 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14568 Z= 0.117 Angle : 0.550 5.349 19922 Z= 0.278 Chirality : 0.042 0.145 2394 Planarity : 0.006 0.055 2544 Dihedral : 4.554 25.532 2014 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.63 % Allowed : 6.19 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 1862 helix: 1.98 (0.18), residues: 826 sheet: 0.35 (0.30), residues: 268 loop : 0.06 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPCT 151 HIS 0.005 0.001 HISCU 299 PHE 0.010 0.001 PHECV 79 TYR 0.009 0.001 TYRCT 222 ARG 0.010 0.001 ARGCV 270 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 763) hydrogen bonds : angle 4.54751 ( 2193) covalent geometry : bond 0.00262 (14568) covalent geometry : angle 0.54961 (19922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 1.622 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6437 (ptt) REVERT: CT 307 TRP cc_start: 0.8446 (m100) cc_final: 0.8223 (m100) REVERT: CV 57 MET cc_start: 0.7493 (mmm) cc_final: 0.7205 (mtm) REVERT: CV 449 ASP cc_start: 0.7264 (m-30) cc_final: 0.7032 (m-30) REVERT: CU 1 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6512 (ptt) REVERT: CU 303 GLN cc_start: 0.8759 (mp10) cc_final: 0.8462 (mp10) REVERT: CW 57 MET cc_start: 0.7832 (mtm) cc_final: 0.7360 (mmm) REVERT: CW 65 HIS cc_start: 0.7161 (m-70) cc_final: 0.6484 (t-90) REVERT: CW 449 ASP cc_start: 0.7282 (m-30) cc_final: 0.7030 (m-30) outliers start: 10 outliers final: 3 residues processed: 147 average time/residue: 1.1144 time to fit residues: 183.1014 Evaluate side-chains 122 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 1 MET Chi-restraints excluded: chain CT residue 273 PHE Chi-restraints excluded: chain CV residue 540 ASP Chi-restraints excluded: chain CU residue 1 MET Chi-restraints excluded: chain CW residue 540 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 161 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 101 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CT 63 GLN CT 64 HIS ** CT 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109354 restraints weight = 22048.622| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.36 r_work: 0.3244 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14568 Z= 0.207 Angle : 0.616 6.455 19922 Z= 0.310 Chirality : 0.046 0.144 2394 Planarity : 0.006 0.053 2544 Dihedral : 4.520 22.675 2010 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.01 % Allowed : 7.40 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.19), residues: 1862 helix: 2.10 (0.18), residues: 818 sheet: 0.39 (0.30), residues: 274 loop : 0.12 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPCT 151 HIS 0.007 0.001 HISCU 299 PHE 0.021 0.002 PHECU 273 TYR 0.014 0.002 TYRCU 36 ARG 0.006 0.001 ARGCV 584 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 763) hydrogen bonds : angle 4.62510 ( 2193) covalent geometry : bond 0.00501 (14568) covalent geometry : angle 0.61569 (19922) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6529 (ptt) REVERT: CT 63 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8274 (mm110) REVERT: CV 449 ASP cc_start: 0.7411 (m-30) cc_final: 0.7080 (m-30) REVERT: CW 57 MET cc_start: 0.7924 (mtm) cc_final: 0.7678 (mmm) REVERT: CW 65 HIS cc_start: 0.7057 (m-70) cc_final: 0.6506 (t-90) REVERT: CW 445 LYS cc_start: 0.7650 (ttmm) cc_final: 0.7195 (tppt) REVERT: CW 449 ASP cc_start: 0.7412 (m-30) cc_final: 0.7048 (m-30) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 1.1437 time to fit residues: 167.8469 Evaluate side-chains 124 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 1 MET Chi-restraints excluded: chain CT residue 164 GLU Chi-restraints excluded: chain CT residue 273 PHE Chi-restraints excluded: chain CV residue 350 ILE Chi-restraints excluded: chain CV residue 540 ASP Chi-restraints excluded: chain CU residue 1 MET Chi-restraints excluded: chain CU residue 164 GLU Chi-restraints excluded: chain CU residue 188 SER Chi-restraints excluded: chain CU residue 273 PHE Chi-restraints excluded: chain CW residue 350 ILE Chi-restraints excluded: chain CW residue 540 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 83 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 169 optimal weight: 0.0470 chunk 174 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 176 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CT 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CV 32 HIS ** CU 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 207 ASN CU 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.129311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111278 restraints weight = 21980.686| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.38 r_work: 0.3259 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14568 Z= 0.137 Angle : 0.549 6.112 19922 Z= 0.277 Chirality : 0.043 0.142 2394 Planarity : 0.005 0.051 2544 Dihedral : 4.322 22.305 2010 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.33 % Allowed : 8.72 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 1862 helix: 2.41 (0.18), residues: 820 sheet: 0.42 (0.29), residues: 270 loop : 0.26 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPCT 206 HIS 0.005 0.001 HISCU 299 PHE 0.019 0.001 PHECU 273 TYR 0.011 0.001 TYRCU 28 ARG 0.010 0.000 ARGCW 572 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 763) hydrogen bonds : angle 4.39668 ( 2193) covalent geometry : bond 0.00325 (14568) covalent geometry : angle 0.54911 (19922) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6379 (ptt) REVERT: CT 63 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8363 (mm110) REVERT: CV 449 ASP cc_start: 0.7356 (m-30) cc_final: 0.7030 (m-30) REVERT: CU 261 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: CW 57 MET cc_start: 0.7887 (mtm) cc_final: 0.7573 (mmm) REVERT: CW 65 HIS cc_start: 0.7084 (m-70) cc_final: 0.6553 (t-90) REVERT: CW 449 ASP cc_start: 0.7365 (m-30) cc_final: 0.7037 (m-30) outliers start: 21 outliers final: 6 residues processed: 133 average time/residue: 1.0630 time to fit residues: 159.5768 Evaluate side-chains 115 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 1 MET Chi-restraints excluded: chain CT residue 164 GLU Chi-restraints excluded: chain CV residue 540 ASP Chi-restraints excluded: chain CU residue 135 THR Chi-restraints excluded: chain CU residue 188 SER Chi-restraints excluded: chain CU residue 261 GLU Chi-restraints excluded: chain CW residue 376 SER Chi-restraints excluded: chain CW residue 540 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 56 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CT 64 HIS ** CT 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CV 32 HIS ** CU 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN CU 376 ASN CW 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110877 restraints weight = 22061.873| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.36 r_work: 0.3252 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14568 Z= 0.143 Angle : 0.549 6.626 19922 Z= 0.275 Chirality : 0.043 0.141 2394 Planarity : 0.005 0.050 2544 Dihedral : 4.249 22.058 2010 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.45 % Allowed : 9.92 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 1862 helix: 2.44 (0.18), residues: 822 sheet: 0.37 (0.29), residues: 272 loop : 0.32 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPCT 206 HIS 0.005 0.001 HISCU 299 PHE 0.009 0.001 PHECV 79 TYR 0.011 0.001 TYRCT 28 ARG 0.004 0.000 ARGCW 567 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 763) hydrogen bonds : angle 4.34979 ( 2193) covalent geometry : bond 0.00345 (14568) covalent geometry : angle 0.54896 (19922) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6506 (ptt) REVERT: CT 63 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8415 (mm-40) REVERT: CV 449 ASP cc_start: 0.7351 (m-30) cc_final: 0.7004 (m-30) REVERT: CU 1 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6862 (ptt) REVERT: CW 57 MET cc_start: 0.7908 (mtm) cc_final: 0.7575 (mmm) REVERT: CW 65 HIS cc_start: 0.7066 (m-70) cc_final: 0.6519 (t-90) REVERT: CW 449 ASP cc_start: 0.7383 (m-30) cc_final: 0.7033 (m-30) outliers start: 23 outliers final: 11 residues processed: 129 average time/residue: 1.1257 time to fit residues: 161.8409 Evaluate side-chains 122 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 1 MET Chi-restraints excluded: chain CT residue 273 PHE Chi-restraints excluded: chain CV residue 350 ILE Chi-restraints excluded: chain CV residue 435 ILE Chi-restraints excluded: chain CV residue 540 ASP Chi-restraints excluded: chain CU residue 1 MET Chi-restraints excluded: chain CU residue 135 THR Chi-restraints excluded: chain CU residue 164 GLU Chi-restraints excluded: chain CU residue 188 SER Chi-restraints excluded: chain CW residue 350 ILE Chi-restraints excluded: chain CW residue 376 SER Chi-restraints excluded: chain CW residue 435 ILE Chi-restraints excluded: chain CW residue 540 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 139 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 120 optimal weight: 0.0020 chunk 53 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 133 optimal weight: 0.0270 chunk 92 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 overall best weight: 0.4848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CT 64 HIS CV 32 HIS CV 226 ASN ** CU 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN CU 376 ASN CW 32 HIS CW 226 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113161 restraints weight = 22065.078| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.37 r_work: 0.3298 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14568 Z= 0.108 Angle : 0.513 6.703 19922 Z= 0.257 Chirality : 0.042 0.139 2394 Planarity : 0.005 0.048 2544 Dihedral : 4.074 21.907 2010 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.39 % Allowed : 10.87 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 2.09 (0.20), residues: 1862 helix: 2.70 (0.18), residues: 820 sheet: 0.40 (0.30), residues: 270 loop : 0.39 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPCT 206 HIS 0.005 0.001 HISCU 299 PHE 0.009 0.001 PHECV 79 TYR 0.010 0.001 TYRCU 28 ARG 0.006 0.000 ARGCW 567 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 763) hydrogen bonds : angle 4.17729 ( 2193) covalent geometry : bond 0.00250 (14568) covalent geometry : angle 0.51320 (19922) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.733 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6245 (ptt) REVERT: CT 63 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8408 (mm-40) REVERT: CV 449 ASP cc_start: 0.7328 (m-30) cc_final: 0.6962 (m-30) REVERT: CU 1 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6467 (ptt) REVERT: CU 109 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8437 (mtm) REVERT: CW 65 HIS cc_start: 0.7068 (m-70) cc_final: 0.6522 (t-90) REVERT: CW 449 ASP cc_start: 0.7421 (m-30) cc_final: 0.7113 (m-30) outliers start: 22 outliers final: 9 residues processed: 127 average time/residue: 1.0094 time to fit residues: 144.7640 Evaluate side-chains 117 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 1 MET Chi-restraints excluded: chain CV residue 435 ILE Chi-restraints excluded: chain CV residue 540 ASP Chi-restraints excluded: chain CU residue 1 MET Chi-restraints excluded: chain CU residue 108 LEU Chi-restraints excluded: chain CU residue 109 MET Chi-restraints excluded: chain CU residue 135 THR Chi-restraints excluded: chain CU residue 164 GLU Chi-restraints excluded: chain CU residue 188 SER Chi-restraints excluded: chain CU residue 316 VAL Chi-restraints excluded: chain CW residue 435 ILE Chi-restraints excluded: chain CW residue 540 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 114 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CT 64 HIS CV 226 ASN ** CU 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN CU 376 ASN CW 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109716 restraints weight = 22308.342| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.39 r_work: 0.3250 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14568 Z= 0.173 Angle : 0.569 7.328 19922 Z= 0.284 Chirality : 0.044 0.138 2394 Planarity : 0.005 0.049 2544 Dihedral : 4.229 21.575 2010 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.64 % Allowed : 11.31 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.19), residues: 1862 helix: 2.45 (0.18), residues: 822 sheet: 0.55 (0.30), residues: 262 loop : 0.42 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPCT 206 HIS 0.006 0.001 HISCU 299 PHE 0.010 0.001 PHECT 6 TYR 0.012 0.001 TYRCT 28 ARG 0.004 0.000 ARGCV 8 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 763) hydrogen bonds : angle 4.35948 ( 2193) covalent geometry : bond 0.00422 (14568) covalent geometry : angle 0.56945 (19922) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6556 (ptt) REVERT: CT 109 MET cc_start: 0.8757 (mtp) cc_final: 0.8553 (mtm) REVERT: CV 449 ASP cc_start: 0.7434 (m-30) cc_final: 0.7048 (m-30) REVERT: CU 1 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6658 (ptt) REVERT: CU 307 TRP cc_start: 0.8419 (m100) cc_final: 0.8201 (m100) REVERT: CW 57 MET cc_start: 0.7866 (mtm) cc_final: 0.7460 (mmm) REVERT: CW 65 HIS cc_start: 0.7085 (m-70) cc_final: 0.6520 (t-90) REVERT: CW 449 ASP cc_start: 0.7450 (m-30) cc_final: 0.7097 (m-30) outliers start: 26 outliers final: 12 residues processed: 133 average time/residue: 0.9795 time to fit residues: 146.8799 Evaluate side-chains 122 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 1 MET Chi-restraints excluded: chain CV residue 350 ILE Chi-restraints excluded: chain CV residue 435 ILE Chi-restraints excluded: chain CV residue 540 ASP Chi-restraints excluded: chain CU residue 1 MET Chi-restraints excluded: chain CU residue 108 LEU Chi-restraints excluded: chain CU residue 135 THR Chi-restraints excluded: chain CU residue 164 GLU Chi-restraints excluded: chain CU residue 188 SER Chi-restraints excluded: chain CU residue 267 VAL Chi-restraints excluded: chain CU residue 316 VAL Chi-restraints excluded: chain CW residue 376 SER Chi-restraints excluded: chain CW residue 435 ILE Chi-restraints excluded: chain CW residue 540 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 111 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CT 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 64 HIS ** CU 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN CU 376 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108455 restraints weight = 22282.013| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.39 r_work: 0.3221 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14568 Z= 0.188 Angle : 0.591 8.024 19922 Z= 0.297 Chirality : 0.045 0.141 2394 Planarity : 0.005 0.051 2544 Dihedral : 4.352 22.648 2010 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.39 % Allowed : 12.01 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 1862 helix: 2.33 (0.18), residues: 820 sheet: 0.53 (0.30), residues: 260 loop : 0.36 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPCT 206 HIS 0.006 0.001 HISCU 299 PHE 0.011 0.001 PHECT 6 TYR 0.012 0.002 TYRCT 28 ARG 0.014 0.001 ARGCW 567 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 763) hydrogen bonds : angle 4.45847 ( 2193) covalent geometry : bond 0.00459 (14568) covalent geometry : angle 0.59149 (19922) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: CV 449 ASP cc_start: 0.7465 (m-30) cc_final: 0.7099 (m-30) REVERT: CW 57 MET cc_start: 0.7880 (mtm) cc_final: 0.7658 (mmm) REVERT: CW 65 HIS cc_start: 0.7076 (m-70) cc_final: 0.6496 (t-90) REVERT: CW 449 ASP cc_start: 0.7479 (m-30) cc_final: 0.7117 (m-30) outliers start: 22 outliers final: 16 residues processed: 122 average time/residue: 0.9492 time to fit residues: 132.0386 Evaluate side-chains 119 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 309 ILE Chi-restraints excluded: chain CV residue 350 ILE Chi-restraints excluded: chain CV residue 376 SER Chi-restraints excluded: chain CV residue 435 ILE Chi-restraints excluded: chain CV residue 540 ASP Chi-restraints excluded: chain CU residue 108 LEU Chi-restraints excluded: chain CU residue 135 THR Chi-restraints excluded: chain CU residue 164 GLU Chi-restraints excluded: chain CU residue 188 SER Chi-restraints excluded: chain CU residue 267 VAL Chi-restraints excluded: chain CU residue 309 ILE Chi-restraints excluded: chain CU residue 316 VAL Chi-restraints excluded: chain CW residue 350 ILE Chi-restraints excluded: chain CW residue 376 SER Chi-restraints excluded: chain CW residue 435 ILE Chi-restraints excluded: chain CW residue 540 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.0370 chunk 178 optimal weight: 0.0670 chunk 182 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CT 64 HIS CV 32 HIS ** CU 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN CU 376 ASN CW 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113349 restraints weight = 21986.200| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.38 r_work: 0.3301 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14568 Z= 0.106 Angle : 0.526 7.476 19922 Z= 0.263 Chirality : 0.042 0.140 2394 Planarity : 0.005 0.051 2544 Dihedral : 4.065 21.093 2010 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.01 % Allowed : 12.77 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 2.21 (0.20), residues: 1862 helix: 2.73 (0.18), residues: 822 sheet: 0.55 (0.30), residues: 260 loop : 0.48 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPCT 307 HIS 0.005 0.001 HISCU 299 PHE 0.009 0.001 PHECV 79 TYR 0.011 0.001 TYRCT 28 ARG 0.011 0.000 ARGCW 567 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 763) hydrogen bonds : angle 4.17743 ( 2193) covalent geometry : bond 0.00242 (14568) covalent geometry : angle 0.52594 (19922) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.664 Fit side-chains revert: symmetry clash REVERT: CV 449 ASP cc_start: 0.7412 (m-30) cc_final: 0.7043 (m-30) REVERT: CW 57 MET cc_start: 0.7940 (mtm) cc_final: 0.7678 (mmm) REVERT: CW 65 HIS cc_start: 0.7075 (m-70) cc_final: 0.6520 (t-90) REVERT: CW 449 ASP cc_start: 0.7442 (m-30) cc_final: 0.7153 (m-30) outliers start: 16 outliers final: 7 residues processed: 125 average time/residue: 0.9179 time to fit residues: 131.1220 Evaluate side-chains 116 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 161 SER Chi-restraints excluded: chain CV residue 435 ILE Chi-restraints excluded: chain CV residue 540 ASP Chi-restraints excluded: chain CU residue 164 GLU Chi-restraints excluded: chain CU residue 316 VAL Chi-restraints excluded: chain CW residue 435 ILE Chi-restraints excluded: chain CW residue 540 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 5 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CT 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 64 HIS CV 32 HIS ** CU 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN CW 32 HIS CW 226 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112378 restraints weight = 22040.260| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.38 r_work: 0.3288 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14568 Z= 0.120 Angle : 0.542 7.705 19922 Z= 0.270 Chirality : 0.042 0.137 2394 Planarity : 0.005 0.048 2544 Dihedral : 4.049 22.836 2010 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.63 % Allowed : 13.34 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 2.20 (0.19), residues: 1862 helix: 2.71 (0.18), residues: 822 sheet: 0.59 (0.29), residues: 262 loop : 0.48 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPCT 307 HIS 0.005 0.001 HISCU 299 PHE 0.009 0.001 PHECV 79 TYR 0.011 0.001 TYRCT 28 ARG 0.011 0.000 ARGCW 567 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 763) hydrogen bonds : angle 4.18877 ( 2193) covalent geometry : bond 0.00287 (14568) covalent geometry : angle 0.54187 (19922) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 1.751 Fit side-chains revert: symmetry clash REVERT: CV 449 ASP cc_start: 0.7445 (m-30) cc_final: 0.7067 (m-30) REVERT: CW 57 MET cc_start: 0.7931 (mtm) cc_final: 0.7661 (mmm) REVERT: CW 65 HIS cc_start: 0.7104 (m-70) cc_final: 0.6544 (t-90) REVERT: CW 449 ASP cc_start: 0.7475 (m-30) cc_final: 0.7176 (m-30) outliers start: 10 outliers final: 8 residues processed: 120 average time/residue: 0.9487 time to fit residues: 129.4316 Evaluate side-chains 117 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CV residue 435 ILE Chi-restraints excluded: chain CV residue 540 ASP Chi-restraints excluded: chain CU residue 108 LEU Chi-restraints excluded: chain CU residue 164 GLU Chi-restraints excluded: chain CU residue 294 MET Chi-restraints excluded: chain CU residue 316 VAL Chi-restraints excluded: chain CW residue 435 ILE Chi-restraints excluded: chain CW residue 540 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 62 optimal weight: 0.0870 chunk 159 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CT 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN CU 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.130394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112617 restraints weight = 22216.842| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.39 r_work: 0.3291 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14568 Z= 0.118 Angle : 0.535 7.721 19922 Z= 0.267 Chirality : 0.042 0.138 2394 Planarity : 0.005 0.047 2544 Dihedral : 4.032 22.168 2010 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.88 % Allowed : 13.40 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 2.21 (0.20), residues: 1862 helix: 2.71 (0.18), residues: 822 sheet: 0.59 (0.29), residues: 262 loop : 0.49 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPCT 307 HIS 0.004 0.001 HISCU 299 PHE 0.009 0.001 PHECV 79 TYR 0.011 0.001 TYRCT 28 ARG 0.011 0.000 ARGCW 567 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 763) hydrogen bonds : angle 4.17138 ( 2193) covalent geometry : bond 0.00280 (14568) covalent geometry : angle 0.53505 (19922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7730.65 seconds wall clock time: 134 minutes 36.08 seconds (8076.08 seconds total)