Starting phenix.real_space_refine on Wed Mar 4 03:53:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ahd_11783/03_2026/7ahd_11783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ahd_11783/03_2026/7ahd_11783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ahd_11783/03_2026/7ahd_11783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ahd_11783/03_2026/7ahd_11783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ahd_11783/03_2026/7ahd_11783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ahd_11783/03_2026/7ahd_11783.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 50 5.16 5 C 6805 2.51 5 N 1762 2.21 5 O 1939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10562 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4170 Classifications: {'peptide': 547} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 525} Chain breaks: 2 Chain: "D" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2069 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 8, 'TRANS': 251} Chain: "B" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2184 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 12, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'BET': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.35, per 1000 atoms: 0.22 Number of scatterers: 10562 At special positions: 0 Unit cell: (92.092, 83.996, 136.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 6 15.00 O 1939 8.00 N 1762 7.00 C 6805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 431.5 milliseconds 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 8 sheets defined 69.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.505A pdb=" N ILE C 34 " --> pdb=" O PRO C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 137 through 153 removed outlier: 3.548A pdb=" N ARG C 141 " --> pdb=" O PRO C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.640A pdb=" N LYS C 158 " --> pdb=" O LEU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 166 through 181 removed outlier: 3.771A pdb=" N ASN C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 214 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.603A pdb=" N ALA C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.735A pdb=" N ILE C 252 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 26 Processing helix chain 'A' and resid 27 through 51 removed outlier: 3.551A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 Processing helix chain 'A' and resid 72 through 89 Processing helix chain 'A' and resid 90 through 122 Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 122 through 139 removed outlier: 4.033A pdb=" N LYS A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Proline residue: A 131 - end of helix Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 155 through 181 removed outlier: 4.253A pdb=" N GLY A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.567A pdb=" N VAL A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 204 through 227 removed outlier: 5.215A pdb=" N GLY A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 238 through 250 removed outlier: 4.078A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 275 Processing helix chain 'A' and resid 290 through 309 Processing helix chain 'A' and resid 330 through 346 Processing helix chain 'A' and resid 357 through 367 Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 423 through 426 removed outlier: 3.772A pdb=" N ASN A 426 " --> pdb=" O ASN A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 518 through 523 removed outlier: 3.695A pdb=" N GLU A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 532 removed outlier: 4.246A pdb=" N VAL A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 550 removed outlier: 3.734A pdb=" N GLY A 550 " --> pdb=" O ASP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 564 Processing helix chain 'A' and resid 564 through 572 removed outlier: 3.528A pdb=" N VAL A 568 " --> pdb=" O HIS A 564 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 30 through 39 removed outlier: 3.505A pdb=" N ILE D 34 " --> pdb=" O PRO D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 137 through 153 removed outlier: 3.549A pdb=" N ARG D 141 " --> pdb=" O PRO D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.639A pdb=" N LYS D 158 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 166 through 181 removed outlier: 3.769A pdb=" N ASN D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 214 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.580A pdb=" N ALA D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.735A pdb=" N ILE D 252 " --> pdb=" O GLY D 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 26 Processing helix chain 'B' and resid 26 through 51 Processing helix chain 'B' and resid 52 through 69 Processing helix chain 'B' and resid 72 through 89 Processing helix chain 'B' and resid 90 through 121 Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 122 through 139 removed outlier: 3.638A pdb=" N ALA B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'B' and resid 156 through 180 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 204 through 227 removed outlier: 5.701A pdb=" N GLY B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.152A pdb=" N GLY B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 275 removed outlier: 3.540A pdb=" N GLY B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 310 Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 51 removed outlier: 6.393A pdb=" N GLY C 43 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE C 13 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR C 45 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR C 11 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR C 47 " --> pdb=" O HIS C 9 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS C 9 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU C 10 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER C 82 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 108 through 111 removed outlier: 6.114A pdb=" N SER C 109 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ASP C 189 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 111 " --> pdb=" O ASP C 189 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU C 186 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL C 221 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N MET C 188 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 234 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C 245 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS C 239 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 328 removed outlier: 6.625A pdb=" N VAL A 323 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR A 354 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 325 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU A 356 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR A 327 " --> pdb=" O LEU A 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 378 removed outlier: 3.654A pdb=" N SER A 375 " --> pdb=" O ASN A 512 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASN A 512 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP A 377 " --> pdb=" O ASN A 510 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN A 510 " --> pdb=" O TRP A 377 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE A 511 " --> pdb=" O ASN A 399 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY A 397 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 515 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU A 395 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 481 through 485 Processing sheet with id=AA6, first strand: chain 'A' and resid 428 through 430 removed outlier: 3.619A pdb=" N VAL A 458 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 42 through 51 removed outlier: 6.393A pdb=" N GLY D 43 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE D 13 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR D 45 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR D 11 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N THR D 47 " --> pdb=" O HIS D 9 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS D 9 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU D 10 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER D 82 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 108 through 111 removed outlier: 6.114A pdb=" N SER D 109 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP D 189 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL D 111 " --> pdb=" O ASP D 189 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU D 186 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL D 221 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N MET D 188 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 234 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN D 245 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LYS D 239 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1864 1.32 - 1.45: 2492 1.45 - 1.57: 6279 1.57 - 1.70: 1 1.70 - 1.82: 106 Bond restraints: 10742 Sorted by residual: bond pdb=" O5' ATP C 501 " pdb=" PA ATP C 501 " ideal model delta sigma weight residual 1.579 1.820 -0.241 1.10e-02 8.26e+03 4.80e+02 bond pdb=" O5' ATP D 501 " pdb=" PA ATP D 501 " ideal model delta sigma weight residual 1.579 1.819 -0.240 1.10e-02 8.26e+03 4.78e+02 bond pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 1.592 1.784 -0.192 1.10e-02 8.26e+03 3.04e+02 bond pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 1.592 1.783 -0.191 1.10e-02 8.26e+03 3.03e+02 bond pdb=" C5' ATP D 501 " pdb=" O5' ATP D 501 " ideal model delta sigma weight residual 1.443 1.344 0.099 1.00e-02 1.00e+04 9.71e+01 ... (remaining 10737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.85: 14507 6.85 - 13.69: 21 13.69 - 20.54: 12 20.54 - 27.38: 0 27.38 - 34.23: 4 Bond angle restraints: 14544 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 105.64 34.23 1.00e+00 1.00e+00 1.17e+03 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 105.68 34.19 1.00e+00 1.00e+00 1.17e+03 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 105.44 31.39 1.00e+00 1.00e+00 9.85e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 105.47 31.36 1.00e+00 1.00e+00 9.83e+02 angle pdb=" C5' ATP D 501 " pdb=" O5' ATP D 501 " pdb=" PA ATP D 501 " ideal model delta sigma weight residual 121.27 104.61 16.66 1.00e+00 1.00e+00 2.78e+02 ... (remaining 14539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 5897 16.69 - 33.38: 477 33.38 - 50.06: 96 50.06 - 66.75: 39 66.75 - 83.44: 6 Dihedral angle restraints: 6515 sinusoidal: 2636 harmonic: 3879 Sorted by residual: dihedral pdb=" CA TRP A 535 " pdb=" C TRP A 535 " pdb=" N THR A 536 " pdb=" CA THR A 536 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLN C 215 " pdb=" C GLN C 215 " pdb=" N LYS C 216 " pdb=" CA LYS C 216 " ideal model delta harmonic sigma weight residual -180.00 -160.64 -19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA GLN D 215 " pdb=" C GLN D 215 " pdb=" N LYS D 216 " pdb=" CA LYS D 216 " ideal model delta harmonic sigma weight residual 180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 6512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1686 0.106 - 0.212: 41 0.212 - 0.317: 0 0.317 - 0.423: 0 0.423 - 0.529: 2 Chirality restraints: 1729 Sorted by residual: chirality pdb=" CB THR D 122 " pdb=" CA THR D 122 " pdb=" OG1 THR D 122 " pdb=" CG2 THR D 122 " both_signs ideal model delta sigma weight residual False 2.55 2.02 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CB THR C 122 " pdb=" CA THR C 122 " pdb=" OG1 THR C 122 " pdb=" CG2 THR C 122 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CA LEU D 225 " pdb=" N LEU D 225 " pdb=" C LEU D 225 " pdb=" CB LEU D 225 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1726 not shown) Planarity restraints: 1805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 142 " 0.109 9.50e-02 1.11e+02 5.50e-02 9.22e+00 pdb=" NE ARG C 142 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C 142 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG C 142 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C 142 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 142 " 0.108 9.50e-02 1.11e+02 5.44e-02 9.15e+00 pdb=" NE ARG D 142 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 142 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG D 142 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG D 142 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 260 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C TYR C 260 " 0.041 2.00e-02 2.50e+03 pdb=" O TYR C 260 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL C 261 " -0.014 2.00e-02 2.50e+03 ... (remaining 1802 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1554 2.75 - 3.29: 11258 3.29 - 3.83: 17215 3.83 - 4.36: 21438 4.36 - 4.90: 37182 Nonbonded interactions: 88647 Sorted by model distance: nonbonded pdb=" OD1 ASP A 134 " pdb=" NH2 ARG A 173 " model vdw 2.215 3.120 nonbonded pdb=" NZ LYS A 321 " pdb=" O GLY A 348 " model vdw 2.216 3.120 nonbonded pdb=" NE2 GLN A 385 " pdb=" O GLN B 248 " model vdw 2.228 3.120 nonbonded pdb=" OG1 THR B 171 " pdb=" OG1 THR B 220 " model vdw 2.249 3.040 nonbonded pdb=" OG1 THR A 381 " pdb=" OE2 GLU A 509 " model vdw 2.264 3.040 ... (remaining 88642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.130 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.008 0.241 10742 Z= 0.522 Angle : 1.096 34.229 14544 Z= 0.771 Chirality : 0.049 0.529 1729 Planarity : 0.004 0.055 1805 Dihedral : 13.541 83.441 4007 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.79 % Allowed : 1.22 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1347 helix: 0.81 (0.18), residues: 858 sheet: -1.97 (0.44), residues: 117 loop : -1.51 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.002 ARG C 142 TYR 0.012 0.002 TYR A 493 PHE 0.024 0.001 PHE B 161 TRP 0.036 0.002 TRP A 535 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00842 (10742) covalent geometry : angle 1.09630 (14544) hydrogen bonds : bond 0.12772 ( 674) hydrogen bonds : angle 6.30605 ( 1965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.7338 (mmm) cc_final: 0.7100 (mmt) REVERT: A 290 LYS cc_start: 0.4636 (pttm) cc_final: 0.4367 (pttm) REVERT: D 62 LEU cc_start: 0.8074 (mp) cc_final: 0.7595 (mp) REVERT: D 101 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7664 (mt) outliers start: 9 outliers final: 1 residues processed: 178 average time/residue: 0.1300 time to fit residues: 30.7927 Evaluate side-chains 93 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 ASN C 151 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 363 GLN A 382 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119615 restraints weight = 14180.590| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.02 r_work: 0.3331 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10742 Z= 0.147 Angle : 0.591 7.274 14544 Z= 0.307 Chirality : 0.043 0.151 1729 Planarity : 0.005 0.050 1805 Dihedral : 6.813 89.481 1488 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.87 % Allowed : 6.29 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.24), residues: 1347 helix: 1.35 (0.18), residues: 881 sheet: -1.28 (0.46), residues: 119 loop : -1.40 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 201 TYR 0.008 0.001 TYR A 144 PHE 0.021 0.001 PHE B 161 TRP 0.015 0.001 TRP A 535 HIS 0.003 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00338 (10742) covalent geometry : angle 0.59138 (14544) hydrogen bonds : bond 0.03922 ( 674) hydrogen bonds : angle 4.87501 ( 1965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 290 LYS cc_start: 0.4718 (pttm) cc_final: 0.4342 (pttm) REVERT: D 101 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8059 (mp) outliers start: 10 outliers final: 5 residues processed: 125 average time/residue: 0.0986 time to fit residues: 17.7744 Evaluate side-chains 107 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117582 restraints weight = 14745.077| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.14 r_work: 0.3326 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10742 Z= 0.138 Angle : 0.551 8.546 14544 Z= 0.282 Chirality : 0.042 0.225 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.523 82.498 1488 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.92 % Allowed : 7.60 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1347 helix: 1.52 (0.18), residues: 883 sheet: -1.03 (0.48), residues: 117 loop : -1.33 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 180 TYR 0.010 0.001 TYR D 260 PHE 0.016 0.001 PHE B 161 TRP 0.016 0.001 TRP A 535 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00323 (10742) covalent geometry : angle 0.55094 (14544) hydrogen bonds : bond 0.03634 ( 674) hydrogen bonds : angle 4.51337 ( 1965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: C 97 LYS cc_start: 0.7621 (mttt) cc_final: 0.7182 (mtmt) REVERT: A 290 LYS cc_start: 0.4729 (pttm) cc_final: 0.4270 (pttm) REVERT: D 101 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8261 (mp) outliers start: 22 outliers final: 15 residues processed: 130 average time/residue: 0.1028 time to fit residues: 19.2842 Evaluate side-chains 120 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 132 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN C 134 GLN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114605 restraints weight = 14901.081| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.14 r_work: 0.3291 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10742 Z= 0.151 Angle : 0.547 7.692 14544 Z= 0.280 Chirality : 0.042 0.224 1729 Planarity : 0.004 0.054 1805 Dihedral : 6.678 86.260 1488 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.18 % Allowed : 8.65 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1347 helix: 1.56 (0.18), residues: 886 sheet: -1.17 (0.47), residues: 121 loop : -1.30 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 180 TYR 0.009 0.001 TYR A 144 PHE 0.018 0.001 PHE A 151 TRP 0.015 0.001 TRP A 535 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00360 (10742) covalent geometry : angle 0.54723 (14544) hydrogen bonds : bond 0.03565 ( 674) hydrogen bonds : angle 4.45591 ( 1965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.336 Fit side-chains REVERT: C 97 LYS cc_start: 0.7767 (mttt) cc_final: 0.7301 (mtmt) REVERT: C 239 LYS cc_start: 0.6736 (mttp) cc_final: 0.6474 (mttt) REVERT: A 290 LYS cc_start: 0.4555 (pttm) cc_final: 0.4150 (pttm) REVERT: A 471 GLU cc_start: 0.7717 (mp0) cc_final: 0.7174 (mp0) REVERT: D 101 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8206 (mp) outliers start: 25 outliers final: 12 residues processed: 125 average time/residue: 0.0861 time to fit residues: 16.0696 Evaluate side-chains 118 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 13 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 88 optimal weight: 0.0870 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN D 134 GLN D 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.125683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115070 restraints weight = 14946.830| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.15 r_work: 0.3280 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10742 Z= 0.119 Angle : 0.521 7.076 14544 Z= 0.268 Chirality : 0.042 0.264 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.617 87.567 1488 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.01 % Allowed : 10.04 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1347 helix: 1.63 (0.18), residues: 893 sheet: -1.02 (0.48), residues: 121 loop : -1.23 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 180 TYR 0.009 0.001 TYR A 144 PHE 0.014 0.001 PHE B 161 TRP 0.015 0.001 TRP A 535 HIS 0.002 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00273 (10742) covalent geometry : angle 0.52136 (14544) hydrogen bonds : bond 0.03357 ( 674) hydrogen bonds : angle 4.36268 ( 1965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.279 Fit side-chains REVERT: C 97 LYS cc_start: 0.7837 (mttt) cc_final: 0.7416 (mtmt) REVERT: C 213 LYS cc_start: 0.7958 (mttp) cc_final: 0.7672 (mttt) REVERT: C 239 LYS cc_start: 0.6684 (mttp) cc_final: 0.6449 (mttt) REVERT: A 290 LYS cc_start: 0.4467 (pttm) cc_final: 0.4041 (pttm) REVERT: A 471 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: D 101 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8228 (mp) REVERT: D 225 LEU cc_start: 0.8281 (mm) cc_final: 0.8071 (mt) outliers start: 23 outliers final: 14 residues processed: 135 average time/residue: 0.0905 time to fit residues: 17.6368 Evaluate side-chains 125 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 133 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110384 restraints weight = 15344.005| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.17 r_work: 0.3213 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10742 Z= 0.162 Angle : 0.565 8.086 14544 Z= 0.288 Chirality : 0.043 0.259 1729 Planarity : 0.004 0.053 1805 Dihedral : 6.680 84.867 1488 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.01 % Allowed : 10.74 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1347 helix: 1.61 (0.18), residues: 880 sheet: -1.04 (0.48), residues: 121 loop : -1.18 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 180 TYR 0.011 0.001 TYR D 260 PHE 0.015 0.001 PHE C 49 TRP 0.017 0.001 TRP A 535 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00390 (10742) covalent geometry : angle 0.56535 (14544) hydrogen bonds : bond 0.03597 ( 674) hydrogen bonds : angle 4.41916 ( 1965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.340 Fit side-chains REVERT: A 290 LYS cc_start: 0.4555 (pttm) cc_final: 0.4149 (pttm) REVERT: A 471 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: D 101 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8211 (mp) outliers start: 23 outliers final: 16 residues processed: 128 average time/residue: 0.1008 time to fit residues: 18.3295 Evaluate side-chains 122 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 260 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 87 optimal weight: 0.1980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 GLN D 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.099995 restraints weight = 15789.657| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.51 r_work: 0.3031 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10742 Z= 0.135 Angle : 0.548 12.728 14544 Z= 0.277 Chirality : 0.042 0.273 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.634 84.876 1488 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.83 % Allowed : 10.74 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.24), residues: 1347 helix: 1.64 (0.18), residues: 892 sheet: -1.08 (0.47), residues: 121 loop : -1.07 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 180 TYR 0.013 0.001 TYR D 45 PHE 0.014 0.001 PHE C 49 TRP 0.021 0.001 TRP A 535 HIS 0.002 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00319 (10742) covalent geometry : angle 0.54775 (14544) hydrogen bonds : bond 0.03427 ( 674) hydrogen bonds : angle 4.34675 ( 1965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.418 Fit side-chains REVERT: A 471 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: D 101 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8390 (mt) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 0.0926 time to fit residues: 16.6196 Evaluate side-chains 124 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 93 optimal weight: 0.0270 chunk 53 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 ASN C 204 GLN A 87 ASN D 102 GLN D 134 GLN D 181 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112178 restraints weight = 15090.209| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.16 r_work: 0.3237 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10742 Z= 0.114 Angle : 0.522 7.185 14544 Z= 0.268 Chirality : 0.041 0.219 1729 Planarity : 0.004 0.051 1805 Dihedral : 6.534 85.152 1488 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.75 % Allowed : 11.09 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.24), residues: 1347 helix: 1.72 (0.18), residues: 895 sheet: -1.07 (0.47), residues: 121 loop : -0.97 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 180 TYR 0.013 0.001 TYR D 45 PHE 0.013 0.001 PHE B 161 TRP 0.019 0.001 TRP A 535 HIS 0.002 0.000 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00257 (10742) covalent geometry : angle 0.52207 (14544) hydrogen bonds : bond 0.03264 ( 674) hydrogen bonds : angle 4.25795 ( 1965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.323 Fit side-chains REVERT: A 471 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: D 101 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8330 (mp) outliers start: 20 outliers final: 15 residues processed: 129 average time/residue: 0.0872 time to fit residues: 16.6288 Evaluate side-chains 126 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 260 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 15 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 129 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN D 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.099938 restraints weight = 15747.423| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.52 r_work: 0.2992 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10742 Z= 0.135 Angle : 0.543 7.395 14544 Z= 0.274 Chirality : 0.042 0.209 1729 Planarity : 0.004 0.051 1805 Dihedral : 6.517 82.759 1488 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.01 % Allowed : 10.83 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.24), residues: 1347 helix: 1.73 (0.18), residues: 896 sheet: -1.19 (0.50), residues: 108 loop : -0.91 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 180 TYR 0.014 0.001 TYR C 260 PHE 0.013 0.001 PHE C 49 TRP 0.024 0.001 TRP A 535 HIS 0.002 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00318 (10742) covalent geometry : angle 0.54278 (14544) hydrogen bonds : bond 0.03356 ( 674) hydrogen bonds : angle 4.26890 ( 1965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.401 Fit side-chains REVERT: A 347 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.7427 (m90) REVERT: A 471 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: D 101 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8341 (mp) outliers start: 23 outliers final: 17 residues processed: 130 average time/residue: 0.0946 time to fit residues: 17.9957 Evaluate side-chains 128 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110920 restraints weight = 15247.192| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.16 r_work: 0.3220 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10742 Z= 0.127 Angle : 0.558 12.289 14544 Z= 0.279 Chirality : 0.041 0.205 1729 Planarity : 0.004 0.051 1805 Dihedral : 6.503 82.630 1488 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.92 % Allowed : 10.92 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1347 helix: 1.75 (0.18), residues: 896 sheet: -1.23 (0.47), residues: 118 loop : -0.88 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 180 TYR 0.017 0.001 TYR C 260 PHE 0.013 0.001 PHE C 49 TRP 0.026 0.001 TRP A 535 HIS 0.002 0.001 HIS A 564 Details of bonding type rmsd covalent geometry : bond 0.00298 (10742) covalent geometry : angle 0.55813 (14544) hydrogen bonds : bond 0.03326 ( 674) hydrogen bonds : angle 4.26836 ( 1965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.411 Fit side-chains REVERT: A 347 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.7176 (m90) REVERT: A 471 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: D 101 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8298 (mp) outliers start: 22 outliers final: 16 residues processed: 129 average time/residue: 0.0946 time to fit residues: 17.9820 Evaluate side-chains 126 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 0.0050 chunk 118 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 112 optimal weight: 0.0470 overall best weight: 0.5892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN D 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.101071 restraints weight = 15861.885| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.52 r_work: 0.3016 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10742 Z= 0.118 Angle : 0.549 10.861 14544 Z= 0.276 Chirality : 0.041 0.192 1729 Planarity : 0.004 0.051 1805 Dihedral : 6.434 82.672 1488 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.66 % Allowed : 11.44 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1347 helix: 1.82 (0.18), residues: 896 sheet: -1.22 (0.48), residues: 118 loop : -0.83 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 180 TYR 0.016 0.001 TYR C 260 PHE 0.012 0.001 PHE B 161 TRP 0.027 0.001 TRP A 535 HIS 0.001 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00269 (10742) covalent geometry : angle 0.54903 (14544) hydrogen bonds : bond 0.03261 ( 674) hydrogen bonds : angle 4.24954 ( 1965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2002.52 seconds wall clock time: 35 minutes 11.32 seconds (2111.32 seconds total)