Starting phenix.real_space_refine on Thu Jun 12 21:53:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptw_17879/06_2025/8ptw_17879.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptw_17879/06_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_17879/06_2025/8ptw_17879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptw_17879/06_2025/8ptw_17879.map" model { file = "/net/cci-nas-00/data/ceres_data/8ptw_17879/06_2025/8ptw_17879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptw_17879/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.45, 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: 3.46 Conformation dependent library (CDL) restraints added in 1.8 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: 1.56 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: 4.56 Time building geometry restraints manager: 4.10 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: 1.380 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.930 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.460 ------------------------------------------------------------------------------- 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 : 1.685 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: 1.2857 time to fit residues: 258.2821 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 : 1.775 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116231 restraints weight = 21799.821| |-----------------------------------------------------------------------------| 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 4.54750 ( 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 : 1.539 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6436 (ptt) REVERT: CT 307 TRP cc_start: 0.8446 (m100) cc_final: 0.8224 (m100) REVERT: CV 57 MET cc_start: 0.7497 (mmm) cc_final: 0.7209 (mtm) REVERT: CV 449 ASP cc_start: 0.7264 (m-30) cc_final: 0.7032 (m-30) REVERT: CU 1 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6509 (ptt) REVERT: CU 303 GLN cc_start: 0.8759 (mp10) cc_final: 0.8463 (mp10) REVERT: CW 57 MET cc_start: 0.7835 (mtm) cc_final: 0.7363 (mmm) REVERT: CW 65 HIS cc_start: 0.7162 (m-70) cc_final: 0.6485 (t-90) REVERT: CW 449 ASP cc_start: 0.7283 (m-30) cc_final: 0.7030 (m-30) outliers start: 10 outliers final: 3 residues processed: 147 average time/residue: 1.0568 time to fit residues: 173.8367 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 : 1.543 ------------------------------------------------------------------------------- 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: 0.0970 chunk 114 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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** CT 322 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115454 restraints weight = 21887.582| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.37 r_work: 0.3319 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1240 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= 0.116 Angle : 0.529 5.506 19922 Z= 0.265 Chirality : 0.042 0.140 2394 Planarity : 0.005 0.051 2544 Dihedral : 4.214 23.154 2010 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.76 % Allowed : 7.65 % 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: 1.79 (0.19), residues: 1862 helix: 2.40 (0.18), residues: 826 sheet: 0.35 (0.29), residues: 274 loop : 0.23 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPCT 151 HIS 0.004 0.001 HISCU 299 PHE 0.018 0.001 PHECU 273 TYR 0.011 0.001 TYRCU 28 ARG 0.006 0.000 ARGCV 270 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 763) hydrogen bonds : angle 4.35800 ( 2193) covalent geometry : bond 0.00269 (14568) covalent geometry : angle 0.52946 (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: 12 poor density : 127 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6329 (ptt) REVERT: CT 307 TRP cc_start: 0.8467 (m100) cc_final: 0.8243 (m100) REVERT: CV 449 ASP cc_start: 0.7286 (m-30) cc_final: 0.6988 (m-30) REVERT: CU 303 GLN cc_start: 0.8741 (mp10) cc_final: 0.8440 (mp10) REVERT: CW 57 MET cc_start: 0.7845 (mtm) cc_final: 0.7591 (mmm) REVERT: CW 65 HIS cc_start: 0.7164 (m-70) cc_final: 0.6485 (t-90) REVERT: CW 449 ASP cc_start: 0.7328 (m-30) cc_final: 0.7012 (m-30) outliers start: 12 outliers final: 5 residues processed: 132 average time/residue: 1.2409 time to fit residues: 182.2446 Evaluate side-chains 117 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 226 MET Chi-restraints excluded: chain CU residue 273 PHE 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: 0.8980 chunk 120 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 63 GLN ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110072 restraints weight = 21993.377| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.38 r_work: 0.3256 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14568 Z= 0.182 Angle : 0.588 6.664 19922 Z= 0.295 Chirality : 0.045 0.140 2394 Planarity : 0.006 0.052 2544 Dihedral : 4.363 22.443 2010 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.88 % Allowed : 8.79 % Favored : 90.33 % 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: 1.75 (0.19), residues: 1862 helix: 2.32 (0.18), residues: 820 sheet: 0.50 (0.30), residues: 270 loop : 0.22 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPCT 206 HIS 0.006 0.001 HISCU 299 PHE 0.019 0.002 PHECU 273 TYR 0.013 0.002 TYRCT 28 ARG 0.008 0.001 ARGCW 567 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 763) hydrogen bonds : angle 4.48422 ( 2193) covalent geometry : bond 0.00442 (14568) covalent geometry : angle 0.58792 (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 139 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 2.378 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6463 (ptt) REVERT: CV 449 ASP cc_start: 0.7352 (m-30) cc_final: 0.6998 (m-30) REVERT: CU 261 GLU cc_start: 0.8597 (mp0) cc_final: 0.8008 (mp0) REVERT: CW 57 MET cc_start: 0.7923 (mtm) cc_final: 0.7590 (mmm) REVERT: CW 65 HIS cc_start: 0.7065 (m-70) cc_final: 0.6518 (t-90) REVERT: CW 445 LYS cc_start: 0.7662 (ttmm) cc_final: 0.7164 (tppt) REVERT: CW 449 ASP cc_start: 0.7372 (m-30) cc_final: 0.7000 (m-30) outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 1.6384 time to fit residues: 239.5904 Evaluate side-chains 120 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** CT 376 ASN CV 32 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106985 restraints weight = 22210.656| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.37 r_work: 0.3198 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14568 Z= 0.237 Angle : 0.637 7.114 19922 Z= 0.321 Chirality : 0.047 0.144 2394 Planarity : 0.006 0.055 2544 Dihedral : 4.614 21.442 2010 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.77 % Allowed : 9.48 % Favored : 88.75 % 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: 1.50 (0.19), residues: 1862 helix: 2.01 (0.18), residues: 822 sheet: 0.35 (0.30), residues: 268 loop : 0.22 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPCT 206 HIS 0.007 0.001 HISCT 299 PHE 0.021 0.002 PHECU 273 TYR 0.016 0.002 TYRCT 36 ARG 0.008 0.001 ARGCW 572 Details of bonding type rmsd hydrogen bonds : bond 0.05167 ( 763) hydrogen bonds : angle 4.67520 ( 2193) covalent geometry : bond 0.00579 (14568) covalent geometry : angle 0.63690 (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 141 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: CV 449 ASP cc_start: 0.7544 (m-30) cc_final: 0.7175 (m-30) REVERT: CV 573 TYR cc_start: 0.8902 (m-80) cc_final: 0.8654 (m-80) REVERT: CU 63 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8445 (mm110) REVERT: CU 261 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: CW 57 MET cc_start: 0.7953 (mtm) cc_final: 0.7657 (mmm) REVERT: CW 65 HIS cc_start: 0.7084 (m-70) cc_final: 0.6523 (t-90) REVERT: CW 445 LYS cc_start: 0.7791 (ttmm) cc_final: 0.6889 (ttmt) REVERT: CW 449 ASP cc_start: 0.7518 (m-30) cc_final: 0.7159 (m-30) outliers start: 28 outliers final: 18 residues processed: 128 average time/residue: 1.0826 time to fit residues: 156.7395 Evaluate side-chains 126 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 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 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 261 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 139 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 171 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 120 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CW 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112537 restraints weight = 22096.693| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.37 r_work: 0.3289 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1806 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= 0.109 Angle : 0.521 6.884 19922 Z= 0.261 Chirality : 0.042 0.139 2394 Planarity : 0.005 0.051 2544 Dihedral : 4.170 21.910 2010 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.39 % Allowed : 11.19 % Favored : 87.42 % 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: 2.03 (0.20), residues: 1862 helix: 2.58 (0.18), residues: 820 sheet: 0.47 (0.30), residues: 264 loop : 0.39 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPCT 151 HIS 0.005 0.001 HISCU 299 PHE 0.023 0.001 PHECU 273 TYR 0.011 0.001 TYRCU 222 ARG 0.005 0.000 ARGCW 567 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 763) hydrogen bonds : angle 4.24690 ( 2193) covalent geometry : bond 0.00247 (14568) covalent geometry : angle 0.52084 (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 144 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.776 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6384 (ptt) REVERT: CV 449 ASP cc_start: 0.7397 (m-30) cc_final: 0.7031 (m-30) REVERT: CV 573 TYR cc_start: 0.8800 (m-80) cc_final: 0.8556 (m-80) REVERT: CU 1 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6628 (ptt) REVERT: CU 63 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8433 (mm110) REVERT: CU 261 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8221 (mm-30) REVERT: CW 57 MET cc_start: 0.7909 (mtm) cc_final: 0.7541 (mmm) REVERT: CW 65 HIS cc_start: 0.7058 (m-70) cc_final: 0.6502 (t-90) REVERT: CW 449 ASP cc_start: 0.7375 (m-30) cc_final: 0.7022 (m-30) outliers start: 22 outliers final: 8 residues processed: 133 average time/residue: 1.0524 time to fit residues: 158.5202 Evaluate side-chains 123 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 435 ILE Chi-restraints excluded: chain CV residue 540 ASP Chi-restraints excluded: chain CU residue 1 MET Chi-restraints excluded: chain CU residue 188 SER Chi-restraints excluded: chain CU residue 261 GLU Chi-restraints excluded: chain CU residue 273 PHE 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: 2.9990 chunk 92 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 CV 226 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108523 restraints weight = 22237.215| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.36 r_work: 0.3221 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14568 Z= 0.194 Angle : 0.592 7.465 19922 Z= 0.297 Chirality : 0.045 0.140 2394 Planarity : 0.005 0.053 2544 Dihedral : 4.342 21.446 2010 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.39 % Allowed : 11.57 % 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: 1.79 (0.19), residues: 1862 helix: 2.27 (0.18), residues: 828 sheet: 0.41 (0.30), residues: 264 loop : 0.37 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPCT 206 HIS 0.006 0.001 HISCU 299 PHE 0.025 0.002 PHECU 273 TYR 0.012 0.002 TYRCU 36 ARG 0.005 0.001 ARGCW 8 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 763) hydrogen bonds : angle 4.45365 ( 2193) covalent geometry : bond 0.00476 (14568) covalent geometry : angle 0.59212 (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 133 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 2.102 Fit side-chains revert: symmetry clash REVERT: CV 449 ASP cc_start: 0.7486 (m-30) cc_final: 0.7100 (m-30) REVERT: CV 573 TYR cc_start: 0.8825 (m-80) cc_final: 0.8559 (m-80) REVERT: CU 63 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8487 (mm110) REVERT: CW 57 MET cc_start: 0.7917 (mtm) cc_final: 0.7568 (mmm) REVERT: CW 65 HIS cc_start: 0.7069 (m-70) cc_final: 0.6494 (t-90) REVERT: CW 449 ASP cc_start: 0.7475 (m-30) cc_final: 0.7106 (m-30) outliers start: 22 outliers final: 15 residues processed: 123 average time/residue: 1.1079 time to fit residues: 154.0781 Evaluate side-chains 121 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 273 PHE Chi-restraints excluded: chain CT residue 309 ILE Chi-restraints excluded: chain CV residue 20 ASP 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 1 MET Chi-restraints excluded: chain CU residue 108 LEU Chi-restraints excluded: chain CU residue 188 SER Chi-restraints excluded: chain CU residue 273 PHE Chi-restraints excluded: chain CU residue 309 ILE 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: 3.9990 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108836 restraints weight = 22139.053| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.36 r_work: 0.3225 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14568 Z= 0.172 Angle : 0.578 7.923 19922 Z= 0.290 Chirality : 0.044 0.138 2394 Planarity : 0.005 0.053 2544 Dihedral : 4.342 22.324 2010 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.14 % Allowed : 12.07 % Favored : 86.79 % 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: 2.33 (0.18), residues: 820 sheet: 0.40 (0.30), residues: 264 loop : 0.37 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPCT 206 HIS 0.006 0.001 HISCU 299 PHE 0.025 0.001 PHECU 273 TYR 0.011 0.001 TYRCT 28 ARG 0.004 0.000 ARGCW 8 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 763) hydrogen bonds : angle 4.44389 ( 2193) covalent geometry : bond 0.00419 (14568) covalent geometry : angle 0.57835 (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 129 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: CV 449 ASP cc_start: 0.7474 (m-30) cc_final: 0.7103 (m-30) REVERT: CV 573 TYR cc_start: 0.8820 (m-80) cc_final: 0.8531 (m-80) REVERT: CU 63 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8524 (mm110) REVERT: CW 57 MET cc_start: 0.7906 (mtm) cc_final: 0.7553 (mmm) REVERT: CW 65 HIS cc_start: 0.7076 (m-70) cc_final: 0.6498 (t-90) REVERT: CW 449 ASP cc_start: 0.7437 (m-30) cc_final: 0.7076 (m-30) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 1.2308 time to fit residues: 172.5724 Evaluate side-chains 119 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1 MET Chi-restraints excluded: chain CU residue 108 LEU Chi-restraints excluded: chain CU residue 135 THR Chi-restraints excluded: chain CU residue 188 SER 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: 0.0970 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 178 optimal weight: 0.1980 chunk 182 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 179 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 CV 226 ASN ** CU 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 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 = 0.3634 r_free = 0.3634 target = 0.130239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112662 restraints weight = 21936.497| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.34 r_work: 0.3290 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14568 Z= 0.110 Angle : 0.530 7.543 19922 Z= 0.265 Chirality : 0.042 0.139 2394 Planarity : 0.005 0.050 2544 Dihedral : 4.090 22.204 2010 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.14 % Allowed : 12.39 % Favored : 86.47 % 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: 2.14 (0.20), residues: 1862 helix: 2.66 (0.18), residues: 820 sheet: 0.53 (0.30), residues: 260 loop : 0.48 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPCT 206 HIS 0.005 0.001 HISCU 299 PHE 0.028 0.001 PHECU 273 TYR 0.011 0.001 TYRCT 28 ARG 0.009 0.000 ARGCV 567 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 763) hydrogen bonds : angle 4.19879 ( 2193) covalent geometry : bond 0.00256 (14568) covalent geometry : angle 0.52990 (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: 18 poor density : 115 time to evaluate : 1.569 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6738 (ptt) REVERT: CV 449 ASP cc_start: 0.7418 (m-30) cc_final: 0.7042 (m-30) REVERT: CV 573 TYR cc_start: 0.8824 (m-80) cc_final: 0.8550 (m-80) REVERT: CU 1 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6367 (ptt) REVERT: CU 261 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: CW 57 MET cc_start: 0.7910 (mtm) cc_final: 0.7541 (mtm) REVERT: CW 65 HIS cc_start: 0.7092 (m-70) cc_final: 0.6541 (t-90) REVERT: CW 449 ASP cc_start: 0.7438 (m-30) cc_final: 0.7152 (m-30) outliers start: 18 outliers final: 10 residues processed: 125 average time/residue: 0.9631 time to fit residues: 136.8951 Evaluate side-chains 119 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 1 MET Chi-restraints excluded: chain CT residue 161 SER Chi-restraints excluded: chain CT residue 188 SER Chi-restraints excluded: chain CT residue 273 PHE 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 188 SER Chi-restraints excluded: chain CU residue 261 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: 0.6980 chunk 41 optimal weight: 0.0070 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- 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 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 = 0.3601 r_free = 0.3601 target = 0.127678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109954 restraints weight = 22044.640| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.36 r_work: 0.3254 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14568 Z= 0.161 Angle : 0.575 8.128 19922 Z= 0.287 Chirality : 0.044 0.171 2394 Planarity : 0.005 0.051 2544 Dihedral : 4.192 21.361 2010 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.26 % Allowed : 13.15 % Favored : 85.59 % 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: 1.96 (0.19), residues: 1862 helix: 2.41 (0.18), residues: 828 sheet: 0.51 (0.30), residues: 260 loop : 0.45 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPCT 206 HIS 0.005 0.001 HISCU 299 PHE 0.031 0.001 PHECU 273 TYR 0.011 0.001 TYRCT 28 ARG 0.008 0.000 ARGCV 567 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 763) hydrogen bonds : angle 4.33744 ( 2193) covalent geometry : bond 0.00392 (14568) covalent geometry : angle 0.57532 (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 131 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: CT 1 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6522 (ptt) REVERT: CV 449 ASP cc_start: 0.7462 (m-30) cc_final: 0.7081 (m-30) REVERT: CV 573 TYR cc_start: 0.8838 (m-80) cc_final: 0.8544 (m-80) REVERT: CW 65 HIS cc_start: 0.7078 (m-70) cc_final: 0.6505 (t-90) REVERT: CW 449 ASP cc_start: 0.7545 (m-30) cc_final: 0.7208 (m-30) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 1.0319 time to fit residues: 142.4542 Evaluate side-chains 124 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CT residue 1 MET Chi-restraints excluded: chain CT residue 161 SER Chi-restraints excluded: chain CT residue 188 SER Chi-restraints excluded: chain CT residue 309 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 1 MET Chi-restraints excluded: chain CU residue 164 GLU Chi-restraints excluded: chain CU residue 188 SER Chi-restraints excluded: chain CU residue 309 ILE 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: 3.9990 chunk 22 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 139 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 322 ASN CW 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110767 restraints weight = 22172.038| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.36 r_work: 0.3266 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14568 Z= 0.137 Angle : 0.554 8.121 19922 Z= 0.278 Chirality : 0.043 0.140 2394 Planarity : 0.005 0.050 2544 Dihedral : 4.161 22.423 2010 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.01 % Allowed : 13.27 % 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: 2.05 (0.19), residues: 1862 helix: 2.52 (0.18), residues: 822 sheet: 0.54 (0.30), residues: 260 loop : 0.48 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPCT 206 HIS 0.005 0.001 HISCU 299 PHE 0.031 0.001 PHECU 273 TYR 0.011 0.001 TYRCT 28 ARG 0.007 0.000 ARGCV 567 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 763) hydrogen bonds : angle 4.28069 ( 2193) covalent geometry : bond 0.00329 (14568) covalent geometry : angle 0.55371 (19922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8760.76 seconds wall clock time: 153 minutes 26.76 seconds (9206.76 seconds total)