Starting phenix.real_space_refine on Mon Jul 28 20:03:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ahd_11783/07_2025/7ahd_11783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ahd_11783/07_2025/7ahd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ahd_11783/07_2025/7ahd_11783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ahd_11783/07_2025/7ahd_11783.map" model { file = "/net/cci-nas-00/data/ceres_data/7ahd_11783/07_2025/7ahd_11783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ahd_11783/07_2025/7ahd_11783.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.39, per 1000 atoms: 0.60 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: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.28 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: 3.61 Time building geometry restraints manager: 3.04 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: 0.920 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.000 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.980 ------------------------------------------------------------------------------- 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 (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: -0.17 (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 TRP 0.036 0.002 TRP A 535 HIS 0.004 0.001 HIS A 382 PHE 0.024 0.001 PHE B 161 TYR 0.012 0.002 TYR A 493 ARG 0.048 0.002 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.12772 ( 674) hydrogen bonds : angle 6.30605 ( 1965) covalent geometry : bond 0.00842 (10742) covalent geometry : angle 1.09630 (14544) *********************** 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 : 1.205 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.7337 (mmm) cc_final: 0.7101 (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: 0.7667 (mt) outliers start: 9 outliers final: 1 residues processed: 178 average time/residue: 0.3029 time to fit residues: 71.1157 Evaluate side-chains 94 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 113 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 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 75 ASN C 151 ASN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117918 restraints weight = 14219.778| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.03 r_work: 0.3317 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10742 Z= 0.156 Angle : 0.593 7.386 14544 Z= 0.307 Chirality : 0.043 0.151 1729 Planarity : 0.005 0.051 1805 Dihedral : 6.827 88.650 1488 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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 (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: 0.55 (0.24), residues: 1347 helix: 1.31 (0.18), residues: 881 sheet: -1.29 (0.46), residues: 119 loop : -1.39 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 535 HIS 0.003 0.001 HIS A 382 PHE 0.022 0.001 PHE B 161 TYR 0.008 0.001 TYR A 144 ARG 0.004 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 674) hydrogen bonds : angle 4.87542 ( 1965) covalent geometry : bond 0.00358 (10742) covalent geometry : angle 0.59272 (14544) *********************** 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 129 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: C 201 ARG cc_start: 0.7350 (ttp-110) cc_final: 0.7105 (mtm-85) REVERT: A 290 LYS cc_start: 0.4677 (pttm) cc_final: 0.4300 (pttm) REVERT: D 101 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8069 (mp) REVERT: D 201 ARG cc_start: 0.7673 (ttm110) cc_final: 0.7304 (mtm180) outliers start: 10 outliers final: 6 residues processed: 124 average time/residue: 0.2276 time to fit residues: 40.5262 Evaluate side-chains 109 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 396 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 72 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 0.0020 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 ASN C 134 GLN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.123917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113073 restraints weight = 15010.453| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.15 r_work: 0.3263 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2371 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= 0.177 Angle : 0.581 8.539 14544 Z= 0.298 Chirality : 0.044 0.205 1729 Planarity : 0.005 0.052 1805 Dihedral : 6.635 85.359 1488 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.92 % Allowed : 8.21 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.68 (0.24), residues: 1347 helix: 1.38 (0.18), residues: 886 sheet: -1.06 (0.48), residues: 117 loop : -1.37 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 535 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.001 PHE B 161 TYR 0.011 0.002 TYR A 144 ARG 0.004 0.000 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 674) hydrogen bonds : angle 4.56336 ( 1965) covalent geometry : bond 0.00419 (10742) covalent geometry : angle 0.58132 (14544) *********************** 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 141 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: C 97 LYS cc_start: 0.7811 (mttt) cc_final: 0.7585 (pttp) REVERT: C 201 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7570 (mtm-85) REVERT: A 119 MET cc_start: 0.8166 (mtp) cc_final: 0.7899 (mtp) REVERT: A 290 LYS cc_start: 0.4586 (pttm) cc_final: 0.4189 (pttm) REVERT: D 101 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8173 (mp) outliers start: 22 outliers final: 13 residues processed: 131 average time/residue: 0.2323 time to fit residues: 43.8813 Evaluate side-chains 117 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 A residue 309 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 396 LEU 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 84 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3428 r_free = 0.3428 target = 0.120182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109358 restraints weight = 15110.301| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.15 r_work: 0.3210 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10742 Z= 0.186 Angle : 0.580 8.260 14544 Z= 0.297 Chirality : 0.043 0.227 1729 Planarity : 0.004 0.056 1805 Dihedral : 6.741 88.930 1488 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 9.08 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.65 (0.24), residues: 1347 helix: 1.38 (0.18), residues: 879 sheet: -1.18 (0.47), residues: 121 loop : -1.32 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 535 HIS 0.003 0.001 HIS A 347 PHE 0.018 0.001 PHE A 193 TYR 0.010 0.001 TYR A 389 ARG 0.004 0.001 ARG D 230 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 674) hydrogen bonds : angle 4.53774 ( 1965) covalent geometry : bond 0.00453 (10742) covalent geometry : angle 0.58037 (14544) *********************** 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 143 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.166 Fit side-chains REVERT: C 201 ARG cc_start: 0.8015 (ttp-110) cc_final: 0.7518 (mtm-85) REVERT: A 290 LYS cc_start: 0.4674 (pttm) cc_final: 0.4287 (pttm) REVERT: A 471 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: D 101 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8198 (mp) outliers start: 28 outliers final: 14 residues processed: 136 average time/residue: 0.2297 time to fit residues: 44.8240 Evaluate side-chains 119 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 THR 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 309 PHE 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 40 LEU 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 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.121711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110902 restraints weight = 15093.418| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.15 r_work: 0.3218 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3066 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= 0.128 Angle : 0.535 7.525 14544 Z= 0.276 Chirality : 0.042 0.243 1729 Planarity : 0.004 0.053 1805 Dihedral : 6.672 88.688 1488 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.92 % Allowed : 10.04 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.89 (0.24), residues: 1347 helix: 1.52 (0.18), residues: 891 sheet: -1.10 (0.47), residues: 121 loop : -1.19 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 535 HIS 0.002 0.001 HIS A 347 PHE 0.015 0.001 PHE B 161 TYR 0.013 0.001 TYR D 260 ARG 0.003 0.000 ARG C 172 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 674) hydrogen bonds : angle 4.41964 ( 1965) covalent geometry : bond 0.00298 (10742) covalent geometry : angle 0.53479 (14544) *********************** 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 140 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.154 Fit side-chains REVERT: A 276 LEU cc_start: 0.8420 (tp) cc_final: 0.8186 (tt) REVERT: A 290 LYS cc_start: 0.4571 (pttm) cc_final: 0.4150 (pttm) REVERT: A 347 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.7209 (m90) REVERT: A 471 GLU cc_start: 0.7751 (mp0) cc_final: 0.7185 (mp0) REVERT: D 101 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8403 (mt) outliers start: 22 outliers final: 17 residues processed: 133 average time/residue: 0.2342 time to fit residues: 44.8309 Evaluate side-chains 127 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 309 PHE Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 395 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 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 40 LEU 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 46 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 21 optimal weight: 0.0770 chunk 14 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 204 GLN D 102 GLN D 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100785 restraints weight = 15725.305| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.50 r_work: 0.3008 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3234 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= 0.123 Angle : 0.526 7.542 14544 Z= 0.270 Chirality : 0.042 0.247 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.666 87.253 1488 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.75 % Allowed : 11.00 % 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 (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: 0.98 (0.24), residues: 1347 helix: 1.57 (0.18), residues: 893 sheet: -1.19 (0.47), residues: 121 loop : -1.10 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 535 HIS 0.002 0.000 HIS A 347 PHE 0.014 0.001 PHE B 161 TYR 0.013 0.001 TYR D 260 ARG 0.004 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 674) hydrogen bonds : angle 4.33708 ( 1965) covalent geometry : bond 0.00284 (10742) covalent geometry : angle 0.52590 (14544) *********************** 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 139 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.125 Fit side-chains REVERT: C 213 LYS cc_start: 0.8403 (mttt) cc_final: 0.8059 (mttt) REVERT: A 276 LEU cc_start: 0.8384 (tp) cc_final: 0.8114 (tt) REVERT: A 347 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7463 (m90) REVERT: A 471 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: D 101 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8283 (mp) outliers start: 20 outliers final: 15 residues processed: 131 average time/residue: 0.2199 time to fit residues: 41.5828 Evaluate side-chains 127 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 309 PHE Chi-restraints excluded: chain A residue 347 HIS 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 108 MET 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 60 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 134 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110419 restraints weight = 15493.320| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.17 r_work: 0.3214 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10742 Z= 0.131 Angle : 0.536 7.504 14544 Z= 0.275 Chirality : 0.042 0.226 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.619 85.272 1488 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.92 % Allowed : 10.83 % 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 (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: 1.00 (0.24), residues: 1347 helix: 1.59 (0.18), residues: 896 sheet: -1.19 (0.46), residues: 121 loop : -1.11 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 535 HIS 0.002 0.001 HIS A 347 PHE 0.013 0.001 PHE B 161 TYR 0.017 0.001 TYR D 45 ARG 0.004 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 674) hydrogen bonds : angle 4.33305 ( 1965) covalent geometry : bond 0.00308 (10742) covalent geometry : angle 0.53596 (14544) *********************** 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 137 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.109 Fit side-chains REVERT: C 213 LYS cc_start: 0.8131 (mttt) cc_final: 0.7925 (mttt) REVERT: A 276 LEU cc_start: 0.8480 (tp) cc_final: 0.8263 (tt) REVERT: A 347 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.7195 (m90) REVERT: A 471 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: D 101 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8382 (mt) outliers start: 22 outliers final: 17 residues processed: 130 average time/residue: 0.2187 time to fit residues: 41.4373 Evaluate side-chains 129 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 309 PHE Chi-restraints excluded: chain A residue 347 HIS 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 108 MET Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 260 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 38 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.120974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110175 restraints weight = 15261.876| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.16 r_work: 0.3211 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3456 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= 0.129 Angle : 0.534 7.758 14544 Z= 0.273 Chirality : 0.042 0.216 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.538 84.065 1488 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.01 % Allowed : 11.35 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1.06 (0.24), residues: 1347 helix: 1.63 (0.18), residues: 897 sheet: -1.21 (0.46), residues: 121 loop : -1.04 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 535 HIS 0.002 0.001 HIS A 347 PHE 0.018 0.001 PHE A 26 TYR 0.013 0.001 TYR D 45 ARG 0.005 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 674) hydrogen bonds : angle 4.30195 ( 1965) covalent geometry : bond 0.00305 (10742) covalent geometry : angle 0.53377 (14544) *********************** 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: 23 poor density : 111 time to evaluate : 1.364 Fit side-chains REVERT: A 276 LEU cc_start: 0.8491 (tp) cc_final: 0.8289 (tt) REVERT: A 347 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.7184 (m90) REVERT: A 471 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: D 101 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8314 (mp) outliers start: 23 outliers final: 19 residues processed: 126 average time/residue: 0.2395 time to fit residues: 43.8897 Evaluate side-chains 131 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 347 HIS 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 108 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 93 optimal weight: 0.0370 chunk 41 optimal weight: 2.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.109053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.096113 restraints weight = 16153.228| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.62 r_work: 0.2966 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10742 Z= 0.152 Angle : 0.555 8.276 14544 Z= 0.283 Chirality : 0.042 0.207 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.571 82.192 1488 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.18 % Allowed : 11.09 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1.09 (0.24), residues: 1347 helix: 1.70 (0.18), residues: 884 sheet: -1.24 (0.45), residues: 121 loop : -1.06 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 535 HIS 0.002 0.001 HIS A 347 PHE 0.014 0.001 PHE A 193 TYR 0.014 0.002 TYR C 260 ARG 0.006 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 674) hydrogen bonds : angle 4.33583 ( 1965) covalent geometry : bond 0.00364 (10742) covalent geometry : angle 0.55536 (14544) *********************** 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 139 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.370 Fit side-chains REVERT: A 276 LEU cc_start: 0.8378 (tp) cc_final: 0.8176 (tt) REVERT: A 347 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.7420 (m90) REVERT: A 471 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: D 108 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8594 (ptt) REVERT: D 143 LYS cc_start: 0.8649 (tmtt) cc_final: 0.8249 (tppt) REVERT: B 106 LEU cc_start: 0.8960 (tp) cc_final: 0.8402 (mt) outliers start: 25 outliers final: 20 residues processed: 130 average time/residue: 0.2255 time to fit residues: 42.4183 Evaluate side-chains 133 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 186 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 347 HIS 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 108 MET Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 40 LEU 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 17 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.104419 restraints weight = 15613.332| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.19 r_work: 0.3135 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10742 Z= 0.219 Angle : 0.617 8.846 14544 Z= 0.315 Chirality : 0.045 0.239 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.515 86.870 1486 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.27 % Allowed : 11.09 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.91 (0.24), residues: 1347 helix: 1.58 (0.18), residues: 869 sheet: -1.40 (0.45), residues: 121 loop : -1.03 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 535 HIS 0.003 0.001 HIS A 564 PHE 0.019 0.002 PHE A 193 TYR 0.014 0.002 TYR D 260 ARG 0.005 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 674) hydrogen bonds : angle 4.49889 ( 1965) covalent geometry : bond 0.00539 (10742) covalent geometry : angle 0.61731 (14544) ********************** 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 140 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 2.096 Fit side-chains REVERT: A 185 GLU cc_start: 0.7973 (tp30) cc_final: 0.7596 (tp30) REVERT: A 347 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7275 (m90) REVERT: A 471 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: A 505 MET cc_start: 0.7712 (mmm) cc_final: 0.7251 (mmm) REVERT: A 545 LEU cc_start: 0.8499 (mt) cc_final: 0.8283 (tp) REVERT: D 108 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8402 (ptt) REVERT: B 106 LEU cc_start: 0.9077 (tp) cc_final: 0.8475 (mt) REVERT: B 214 MET cc_start: 0.8353 (mmm) cc_final: 0.7683 (mmm) REVERT: B 248 GLN cc_start: 0.8683 (mm110) cc_final: 0.8240 (mm-40) outliers start: 26 outliers final: 21 residues processed: 133 average time/residue: 0.2452 time to fit residues: 48.1591 Evaluate side-chains 135 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 186 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 347 HIS 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 108 MET Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 103 LEU 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 16 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.0010 chunk 108 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- 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** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094659 restraints weight = 16069.273| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.61 r_work: 0.2951 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3772 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= 0.141 Angle : 0.554 8.029 14544 Z= 0.285 Chirality : 0.042 0.258 1729 Planarity : 0.004 0.051 1805 Dihedral : 6.375 83.876 1486 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.18 % Allowed : 11.70 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 1.01 (0.24), residues: 1347 helix: 1.65 (0.18), residues: 885 sheet: -1.43 (0.49), residues: 108 loop : -1.07 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 535 HIS 0.002 0.001 HIS A 347 PHE 0.013 0.001 PHE A 193 TYR 0.015 0.002 TYR C 260 ARG 0.005 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 674) hydrogen bonds : angle 4.41057 ( 1965) covalent geometry : bond 0.00333 (10742) covalent geometry : angle 0.55407 (14544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5277.40 seconds wall clock time: 94 minutes 20.60 seconds (5660.60 seconds total)