Starting phenix.real_space_refine on Fri Feb 14 21:16:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ahd_11783/02_2025/7ahd_11783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ahd_11783/02_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_11783/02_2025/7ahd_11783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ahd_11783/02_2025/7ahd_11783.map" model { file = "/net/cci-nas-00/data/ceres_data/7ahd_11783/02_2025/7ahd_11783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ahd_11783/02_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-5592/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: 6.44, per 1000 atoms: 0.61 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: 2.60 Conformation dependent library (CDL) restraints added in 1.5 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: 1.14 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: 3.58 Time building geometry restraints manager: 3.02 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: 0.730 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.650 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.320 ------------------------------------------------------------------------------- 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= 0.534 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 *********************** 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 : 1.135 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: 0.3011 time to fit residues: 70.4355 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 : 1.239 ------------------------------------------------------------------------------- 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 = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117863 restraints weight = 14219.913| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.03 r_work: 0.3311 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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= 0.231 Angle : 0.593 7.385 14544 Z= 0.307 Chirality : 0.043 0.151 1729 Planarity : 0.005 0.051 1805 Dihedral : 6.827 88.649 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 0.021 0.001 PHE B 161 TYR 0.008 0.001 TYR A 144 ARG 0.004 0.001 ARG D 76 *********************** 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 : 1.209 Fit side-chains revert: symmetry clash REVERT: C 201 ARG cc_start: 0.7371 (ttp-110) cc_final: 0.7130 (mtm-85) REVERT: A 290 LYS cc_start: 0.4719 (pttm) cc_final: 0.4335 (pttm) REVERT: D 101 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8064 (mp) REVERT: D 201 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7328 (mtm180) outliers start: 10 outliers final: 6 residues processed: 124 average time/residue: 0.2327 time to fit residues: 41.3364 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 : 1.306 ------------------------------------------------------------------------------- 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: 3.9990 chunk 63 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 ** 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 = 0.3416 r_free = 0.3416 target = 0.121128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110076 restraints weight = 14868.207| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.17 r_work: 0.3201 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10742 Z= 0.250 Angle : 0.571 8.738 14544 Z= 0.293 Chirality : 0.043 0.214 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.595 84.069 1488 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.92 % Allowed : 8.12 % Favored : 89.96 % 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: 0.73 (0.24), residues: 1347 helix: 1.42 (0.18), residues: 885 sheet: -1.05 (0.48), residues: 117 loop : -1.34 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 535 HIS 0.003 0.001 HIS A 347 PHE 0.016 0.001 PHE B 161 TYR 0.011 0.002 TYR D 260 ARG 0.004 0.000 ARG D 230 *********************** 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 : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 97 LYS cc_start: 0.7902 (mttt) cc_final: 0.7403 (mtmt) REVERT: C 201 ARG cc_start: 0.7753 (ttp-110) cc_final: 0.7508 (mtm-85) REVERT: A 119 MET cc_start: 0.8275 (mtp) cc_final: 0.8070 (mtp) REVERT: A 290 LYS cc_start: 0.4545 (pttm) cc_final: 0.4147 (pttm) REVERT: D 101 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8170 (mp) outliers start: 22 outliers final: 15 residues processed: 132 average time/residue: 0.2366 time to fit residues: 44.9404 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 : 1.285 ------------------------------------------------------------------------------- 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 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 D residue 252 ILE 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: 6.9990 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 0.0010 chunk 23 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 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 = 0.3476 r_free = 0.3476 target = 0.123991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113298 restraints weight = 14872.121| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.15 r_work: 0.3253 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2648 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= 0.211 Angle : 0.537 7.588 14544 Z= 0.276 Chirality : 0.042 0.228 1729 Planarity : 0.004 0.053 1805 Dihedral : 6.596 86.356 1488 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.10 % Allowed : 9.00 % Favored : 88.91 % 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: 0.88 (0.24), residues: 1347 helix: 1.53 (0.18), residues: 886 sheet: -0.97 (0.48), residues: 117 loop : -1.29 (0.34), residues: 344 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 0.019 0.001 PHE A 151 TYR 0.009 0.001 TYR A 144 ARG 0.003 0.000 ARG D 230 *********************** 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 140 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.241 Fit side-chains REVERT: C 97 LYS cc_start: 0.7819 (mttt) cc_final: 0.7404 (mtmt) REVERT: C 201 ARG cc_start: 0.7871 (ttp-110) cc_final: 0.7501 (mtm-85) REVERT: C 239 LYS cc_start: 0.6720 (mttp) cc_final: 0.6483 (mttt) REVERT: A 290 LYS cc_start: 0.4483 (pttm) cc_final: 0.4081 (pttm) REVERT: A 471 GLU cc_start: 0.7762 (mp0) cc_final: 0.7191 (mp0) REVERT: D 101 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8148 (mp) outliers start: 24 outliers final: 11 residues processed: 134 average time/residue: 0.2259 time to fit residues: 44.2644 Evaluate side-chains 117 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 309 PHE 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 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: 2.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3476 r_free = 0.3476 target = 0.123923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113213 restraints weight = 14931.635| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.14 r_work: 0.3255 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2890 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= 0.187 Angle : 0.531 7.231 14544 Z= 0.272 Chirality : 0.042 0.268 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.680 89.584 1488 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.83 % Allowed : 10.13 % 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: 0.95 (0.24), residues: 1347 helix: 1.58 (0.18), residues: 892 sheet: -1.06 (0.48), residues: 121 loop : -1.27 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 535 HIS 0.002 0.001 HIS A 476 PHE 0.014 0.001 PHE B 161 TYR 0.010 0.001 TYR D 260 ARG 0.004 0.000 ARG B 180 *********************** 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 139 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.193 Fit side-chains REVERT: C 97 LYS cc_start: 0.7888 (mttt) cc_final: 0.7474 (mtmt) REVERT: C 224 ASP cc_start: 0.8233 (t0) cc_final: 0.8031 (t0) REVERT: C 239 LYS cc_start: 0.6710 (mttp) cc_final: 0.6471 (mttt) REVERT: A 290 LYS cc_start: 0.4567 (pttm) cc_final: 0.4152 (pttm) REVERT: A 471 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: D 101 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8145 (mp) REVERT: D 251 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7145 (mt-10) REVERT: B 119 MET cc_start: 0.8521 (ttt) cc_final: 0.8313 (ttp) outliers start: 21 outliers final: 14 residues processed: 131 average time/residue: 0.2254 time to fit residues: 42.7634 Evaluate side-chains 123 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN D 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.090679 restraints weight = 16514.310| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.58 r_work: 0.2922 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10742 Z= 0.372 Angle : 0.624 8.465 14544 Z= 0.319 Chirality : 0.045 0.289 1729 Planarity : 0.005 0.055 1805 Dihedral : 6.964 89.550 1488 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.18 % Allowed : 10.74 % Favored : 87.07 % 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: 0.71 (0.24), residues: 1347 helix: 1.42 (0.18), residues: 879 sheet: -1.21 (0.47), residues: 121 loop : -1.27 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 535 HIS 0.004 0.001 HIS A 347 PHE 0.019 0.002 PHE B 193 TYR 0.013 0.002 TYR A 389 ARG 0.006 0.001 ARG B 180 *********************** 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 133 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.154 Fit side-chains REVERT: C 97 LYS cc_start: 0.8081 (mttt) cc_final: 0.7654 (pttp) REVERT: A 347 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7494 (m90) REVERT: A 471 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: B 106 LEU cc_start: 0.8883 (tp) cc_final: 0.8333 (mt) outliers start: 25 outliers final: 15 residues processed: 128 average time/residue: 0.2585 time to fit residues: 46.6288 Evaluate side-chains 119 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 347 HIS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 0.0980 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 363 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 = 0.3389 r_free = 0.3389 target = 0.117397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106510 restraints weight = 15706.779| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.18 r_work: 0.3151 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3453 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= 0.287 Angle : 0.575 8.335 14544 Z= 0.295 Chirality : 0.043 0.227 1729 Planarity : 0.004 0.054 1805 Dihedral : 6.596 87.489 1486 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.10 % Allowed : 10.83 % Favored : 87.07 % 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: 0.77 (0.24), residues: 1347 helix: 1.48 (0.18), residues: 879 sheet: -1.32 (0.46), residues: 121 loop : -1.22 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 535 HIS 0.003 0.001 HIS A 564 PHE 0.016 0.001 PHE C 49 TYR 0.016 0.002 TYR D 260 ARG 0.008 0.001 ARG B 180 *********************** 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 133 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.245 Fit side-chains REVERT: A 347 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.7221 (m90) REVERT: A 471 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: B 106 LEU cc_start: 0.9040 (tp) cc_final: 0.8469 (mt) REVERT: B 214 MET cc_start: 0.8297 (mmm) cc_final: 0.7632 (mmm) outliers start: 24 outliers final: 18 residues processed: 126 average time/residue: 0.2447 time to fit residues: 43.3735 Evaluate side-chains 127 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 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 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 38 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN D 134 GLN D 181 ASN D 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.096899 restraints weight = 15908.737| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.61 r_work: 0.2986 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10742 Z= 0.182 Angle : 0.541 7.818 14544 Z= 0.277 Chirality : 0.042 0.268 1729 Planarity : 0.004 0.052 1805 Dihedral : 6.380 85.483 1486 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.47 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 (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: 0.94 (0.24), residues: 1347 helix: 1.54 (0.18), residues: 896 sheet: -1.40 (0.48), residues: 108 loop : -1.06 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 535 HIS 0.001 0.000 HIS A 347 PHE 0.014 0.001 PHE B 161 TYR 0.014 0.001 TYR D 260 ARG 0.006 0.000 ARG B 180 *********************** 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 139 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.162 Fit side-chains REVERT: A 276 LEU cc_start: 0.8426 (tp) cc_final: 0.8205 (tt) REVERT: A 471 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: A 505 MET cc_start: 0.7865 (mmm) cc_final: 0.7479 (mmm) REVERT: D 108 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8495 (ptt) REVERT: D 134 GLN cc_start: 0.8896 (mt0) cc_final: 0.8636 (mt0) REVERT: B 106 LEU cc_start: 0.8982 (tp) cc_final: 0.8401 (mt) REVERT: B 214 MET cc_start: 0.8263 (mmm) cc_final: 0.7542 (mmm) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 0.2366 time to fit residues: 44.6174 Evaluate side-chains 130 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 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 102 GLN Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 11 ILE 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: 7.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN D 181 ASN D 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106241 restraints weight = 15667.065| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.18 r_work: 0.3154 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10742 Z= 0.291 Angle : 0.589 8.221 14544 Z= 0.300 Chirality : 0.044 0.260 1729 Planarity : 0.004 0.053 1805 Dihedral : 6.420 84.091 1486 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.92 % Allowed : 11.09 % Favored : 86.99 % 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: 0.98 (0.24), residues: 1347 helix: 1.65 (0.18), residues: 868 sheet: -1.47 (0.48), residues: 108 loop : -1.02 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 535 HIS 0.003 0.001 HIS A 347 PHE 0.016 0.001 PHE A 193 TYR 0.016 0.002 TYR D 260 ARG 0.003 0.000 ARG C 172 *********************** 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 132 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 347 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.7186 (m90) REVERT: A 471 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: D 108 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8256 (ptt) REVERT: B 106 LEU cc_start: 0.9059 (tp) cc_final: 0.8485 (mt) REVERT: B 214 MET cc_start: 0.8266 (mmm) cc_final: 0.7630 (mmm) outliers start: 22 outliers final: 19 residues processed: 126 average time/residue: 0.2237 time to fit residues: 40.5775 Evaluate side-chains 129 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 250 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 156 VAL 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 41 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 98 ILE 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: 0.8980 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN D 181 ASN D 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.100899 restraints weight = 15377.046| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.25 r_work: 0.2999 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3702 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= 0.215 Angle : 0.560 7.891 14544 Z= 0.285 Chirality : 0.042 0.250 1729 Planarity : 0.004 0.053 1805 Dihedral : 6.334 83.900 1486 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.57 % Allowed : 11.44 % Favored : 86.99 % 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: 1.02 (0.24), residues: 1347 helix: 1.67 (0.18), residues: 884 sheet: -1.53 (0.46), residues: 118 loop : -1.06 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 535 HIS 0.002 0.001 HIS A 347 PHE 0.014 0.001 PHE C 49 TYR 0.018 0.002 TYR C 260 ARG 0.003 0.000 ARG C 172 ********************** 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 128 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: C 210 LEU cc_start: 0.8674 (tp) cc_final: 0.8441 (tt) REVERT: A 347 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.7254 (m90) REVERT: A 471 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: D 108 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8420 (ptt) REVERT: B 106 LEU cc_start: 0.9038 (tp) cc_final: 0.8453 (mt) REVERT: B 214 MET cc_start: 0.8168 (mmm) cc_final: 0.7465 (mmm) outliers start: 18 outliers final: 15 residues processed: 123 average time/residue: 0.2354 time to fit residues: 42.0439 Evaluate side-chains 126 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 156 VAL 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 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 16 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 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 = 0.3394 r_free = 0.3394 target = 0.117921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107074 restraints weight = 15421.967| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.17 r_work: 0.3167 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3745 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= 0.240 Angle : 0.567 8.308 14544 Z= 0.289 Chirality : 0.043 0.209 1729 Planarity : 0.004 0.053 1805 Dihedral : 6.306 83.488 1486 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.92 % Allowed : 11.27 % Favored : 86.81 % 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: 1.03 (0.24), residues: 1347 helix: 1.67 (0.18), residues: 883 sheet: -1.56 (0.48), residues: 108 loop : -1.04 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 535 HIS 0.002 0.001 HIS A 564 PHE 0.014 0.001 PHE A 193 TYR 0.016 0.002 TYR D 260 ARG 0.003 0.000 ARG D 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4160.03 seconds wall clock time: 75 minutes 0.39 seconds (4500.39 seconds total)