Starting phenix.real_space_refine on Wed Jan 14 00:14:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f1a_28789/01_2026/8f1a_28789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f1a_28789/01_2026/8f1a_28789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f1a_28789/01_2026/8f1a_28789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f1a_28789/01_2026/8f1a_28789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f1a_28789/01_2026/8f1a_28789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f1a_28789/01_2026/8f1a_28789.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6413 2.51 5 N 1750 2.21 5 O 1956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10187 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3446 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain: "B" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3376 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Chain: "K" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3242 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {' MG': 1, 'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.39, per 1000 atoms: 0.23 Number of scatterers: 10187 At special positions: 0 Unit cell: (111.408, 81.024, 111.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 5 15.00 Mg 1 11.99 O 1956 8.00 N 1750 7.00 C 6413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 487.7 milliseconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 46.9% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 3.961A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.341A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.557A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.691A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.655A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.796A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.054A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.787A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.993A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.115A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.113A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 69 through 78 removed outlier: 3.818A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 111 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.552A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.668A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.706A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.003A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.868A pdb=" N ARG B 282 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.638A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.730A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.287A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 424 Processing helix chain 'K' and resid 74 through 79 Processing helix chain 'K' and resid 101 through 105 Processing helix chain 'K' and resid 131 through 140 removed outlier: 3.514A pdb=" N THR K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 150 Processing helix chain 'K' and resid 164 through 170 Processing helix chain 'K' and resid 177 through 190 Processing helix chain 'K' and resid 212 through 229 Processing helix chain 'K' and resid 350 through 365 removed outlier: 3.532A pdb=" N ALA K 354 " --> pdb=" O ASP K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 446 removed outlier: 3.837A pdb=" N GLU K 425 " --> pdb=" O GLU K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 460 removed outlier: 3.727A pdb=" N ASP K 460 " --> pdb=" O PRO K 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 457 through 460' Processing helix chain 'K' and resid 461 through 467 Processing helix chain 'K' and resid 467 through 473 removed outlier: 3.595A pdb=" N PHE K 471 " --> pdb=" O PHE K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 486 through 488 No H-bonds generated for 'chain 'K' and resid 486 through 488' Processing helix chain 'K' and resid 489 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.412A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 removed outlier: 6.733A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.645A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.958A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'K' and resid 124 through 126 removed outlier: 6.551A pdb=" N LEU K 68 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR K 67 " --> pdb=" O VAL K 481 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL K 483 " --> pdb=" O TYR K 67 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG K 69 " --> pdb=" O VAL K 483 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE K 480 " --> pdb=" O LEU K 154 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR K 156 " --> pdb=" O ILE K 480 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ASN K 482 " --> pdb=" O TYR K 156 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR K 158 " --> pdb=" O ASN K 482 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP K 153 " --> pdb=" O SER K 404 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N CYS K 406 " --> pdb=" O TRP K 153 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE K 155 " --> pdb=" O CYS K 406 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 124 through 126 removed outlier: 6.551A pdb=" N LEU K 68 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR K 67 " --> pdb=" O VAL K 481 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL K 483 " --> pdb=" O TYR K 67 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG K 69 " --> pdb=" O VAL K 483 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE K 480 " --> pdb=" O LEU K 154 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR K 156 " --> pdb=" O ILE K 480 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ASN K 482 " --> pdb=" O TYR K 156 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR K 158 " --> pdb=" O ASN K 482 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP K 153 " --> pdb=" O SER K 404 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N CYS K 406 " --> pdb=" O TRP K 153 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE K 155 " --> pdb=" O CYS K 406 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL K 300 " --> pdb=" O VAL K 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 87 through 89 removed outlier: 3.579A pdb=" N CYS K 88 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA K 503 " --> pdb=" O THR K 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 200 through 201 Processing sheet with id=AB1, first strand: chain 'K' and resid 330 through 332 Processing sheet with id=AB2, first strand: chain 'K' and resid 367 through 369 483 hydrogen bonds defined for protein. 1362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.20 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: 1761 1.32 - 1.44: 2737 1.44 - 1.57: 5808 1.57 - 1.69: 12 1.69 - 1.81: 96 Bond restraints: 10414 Sorted by residual: bond pdb=" N ILE K 396 " pdb=" CA ILE K 396 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.18e-02 7.18e+03 9.20e+00 bond pdb=" N VAL K 290 " pdb=" CA VAL K 290 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.27e-02 6.20e+03 7.88e+00 bond pdb=" N ARG K 450 " pdb=" CA ARG K 450 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.19e-02 7.06e+03 7.45e+00 bond pdb=" N VAL K 292 " pdb=" CA VAL K 292 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.07e+00 bond pdb=" N VAL A 344 " pdb=" CA VAL A 344 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 7.02e+00 ... (remaining 10409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 13857 2.41 - 4.83: 240 4.83 - 7.24: 32 7.24 - 9.65: 4 9.65 - 12.06: 1 Bond angle restraints: 14134 Sorted by residual: angle pdb=" N GLN K 445 " pdb=" CA GLN K 445 " pdb=" C GLN K 445 " ideal model delta sigma weight residual 113.88 107.88 6.00 1.23e+00 6.61e-01 2.38e+01 angle pdb=" N GLU K 233 " pdb=" CA GLU K 233 " pdb=" C GLU K 233 " ideal model delta sigma weight residual 114.31 109.03 5.28 1.29e+00 6.01e-01 1.67e+01 angle pdb=" C14 TA1 B 503 " pdb=" C11 TA1 B 503 " pdb=" O04 TA1 B 503 " ideal model delta sigma weight residual 119.42 107.36 12.06 3.00e+00 1.11e-01 1.62e+01 angle pdb=" N ARG K 444 " pdb=" CA ARG K 444 " pdb=" C ARG K 444 " ideal model delta sigma weight residual 113.18 108.69 4.49 1.21e+00 6.83e-01 1.37e+01 angle pdb=" C ASP K 395 " pdb=" CA ASP K 395 " pdb=" CB ASP K 395 " ideal model delta sigma weight residual 116.63 112.34 4.29 1.16e+00 7.43e-01 1.37e+01 ... (remaining 14129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.76: 5956 26.76 - 53.52: 292 53.52 - 80.27: 46 80.27 - 107.03: 8 107.03 - 133.79: 4 Dihedral angle restraints: 6306 sinusoidal: 2616 harmonic: 3690 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -29.19 133.79 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" O2B GDP B 502 " pdb=" O3A GDP B 502 " pdb=" PB GDP B 502 " pdb=" PA GDP B 502 " ideal model delta sinusoidal sigma weight residual 180.00 55.34 124.66 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 168.79 -99.52 1 2.00e+01 2.50e-03 2.80e+01 ... (remaining 6303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1425 0.092 - 0.185: 126 0.185 - 0.277: 3 0.277 - 0.369: 0 0.369 - 0.461: 1 Chirality restraints: 1555 Sorted by residual: chirality pdb=" C18 TA1 B 503 " pdb=" C10 TA1 B 503 " pdb=" C17 TA1 B 503 " pdb=" C20 TA1 B 503 " both_signs ideal model delta sigma weight residual False -3.16 -2.70 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" C02 TA1 B 503 " pdb=" C01 TA1 B 503 " pdb=" C10 TA1 B 503 " pdb=" O02 TA1 B 503 " both_signs ideal model delta sigma weight residual False 2.56 2.77 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C11 TA1 B 503 " pdb=" C10 TA1 B 503 " pdb=" C14 TA1 B 503 " pdb=" C15 TA1 B 503 " both_signs ideal model delta sigma weight residual False 2.83 2.65 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 1552 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 510 " -0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO K 511 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO K 511 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 511 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " -0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO A 89 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 92 " -0.014 2.00e-02 2.50e+03 1.67e-02 4.90e+00 pdb=" CG PHE B 92 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 92 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 92 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 92 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 92 " -0.003 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 105 2.64 - 3.21: 9365 3.21 - 3.77: 15238 3.77 - 4.34: 21034 4.34 - 4.90: 35550 Nonbonded interactions: 81292 Sorted by model distance: nonbonded pdb=" O VAL K 160 " pdb=" OG SER K 163 " model vdw 2.076 3.040 nonbonded pdb=" O THR B 274 " pdb=" O07 TA1 B 503 " model vdw 2.092 3.040 nonbonded pdb=" OG SER B 172 " pdb=" OD1 ASP B 203 " model vdw 2.113 3.040 nonbonded pdb=" O3G GTP A 501 " pdb="MG MG B 501 " model vdw 2.152 2.170 nonbonded pdb=" O GLN K 453 " pdb=" OD1 ASN K 454 " model vdw 2.157 3.040 ... (remaining 81287 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.420 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.990 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 0.005 0.047 10414 Z= 0.245 Angle : 0.780 12.064 14134 Z= 0.424 Chirality : 0.049 0.461 1555 Planarity : 0.005 0.064 1835 Dihedral : 16.308 133.788 3932 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.45 % Allowed : 14.18 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1270 helix: 0.95 (0.23), residues: 493 sheet: 0.47 (0.37), residues: 203 loop : -1.02 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.009 0.001 TYR B 183 PHE 0.039 0.002 PHE B 92 TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS K 323 Details of bonding type rmsd covalent geometry : bond 0.00470 (10414) covalent geometry : angle 0.78020 (14134) hydrogen bonds : bond 0.17155 ( 461) hydrogen bonds : angle 6.49543 ( 1362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 221 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 200 LEU cc_start: 0.8537 (mt) cc_final: 0.8183 (tt) REVERT: K 317 GLU cc_start: 0.6992 (tp30) cc_final: 0.6480 (mm-30) REVERT: K 342 ASP cc_start: 0.7583 (t0) cc_final: 0.7280 (t0) REVERT: K 364 ASN cc_start: 0.7965 (t0) cc_final: 0.7688 (t0) REVERT: K 413 ARG cc_start: 0.6254 (ttt-90) cc_final: 0.6016 (ptm160) REVERT: K 429 ILE cc_start: 0.8825 (mt) cc_final: 0.8483 (mt) REVERT: K 432 SER cc_start: 0.9134 (t) cc_final: 0.8759 (p) outliers start: 5 outliers final: 0 residues processed: 223 average time/residue: 0.1045 time to fit residues: 32.7873 Evaluate side-chains 214 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 424 GLN K 337 ASN ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 ASN K 445 GLN K 446 ASN K 453 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.155303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113801 restraints weight = 13174.853| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.03 r_work: 0.3318 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10414 Z= 0.150 Angle : 0.568 6.717 14134 Z= 0.291 Chirality : 0.044 0.240 1555 Planarity : 0.004 0.051 1835 Dihedral : 8.501 135.471 1512 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.17 % Allowed : 13.46 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1270 helix: 1.67 (0.24), residues: 501 sheet: 0.50 (0.35), residues: 222 loop : -0.88 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 264 TYR 0.011 0.001 TYR B 310 PHE 0.014 0.001 PHE A 67 TRP 0.011 0.001 TRP A 21 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00348 (10414) covalent geometry : angle 0.56771 (14134) hydrogen bonds : bond 0.04733 ( 461) hydrogen bonds : angle 4.65106 ( 1362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7530 (m-80) cc_final: 0.7272 (m-80) REVERT: A 398 MET cc_start: 0.7867 (mtm) cc_final: 0.7623 (ttm) REVERT: B 48 ASN cc_start: 0.8598 (p0) cc_final: 0.8385 (p0) REVERT: B 177 ASP cc_start: 0.7696 (p0) cc_final: 0.7422 (p0) REVERT: K 73 PHE cc_start: 0.7614 (m-80) cc_final: 0.7323 (m-10) REVERT: K 129 GLU cc_start: 0.8334 (mp0) cc_final: 0.7964 (mp0) REVERT: K 342 ASP cc_start: 0.7944 (t0) cc_final: 0.7658 (t0) REVERT: K 415 LYS cc_start: 0.6285 (tmtt) cc_final: 0.5869 (tmmt) REVERT: K 429 ILE cc_start: 0.8678 (mt) cc_final: 0.8241 (mt) REVERT: K 432 SER cc_start: 0.9052 (t) cc_final: 0.8614 (p) REVERT: K 454 ASN cc_start: 0.8060 (m-40) cc_final: 0.7770 (m-40) outliers start: 24 outliers final: 15 residues processed: 229 average time/residue: 0.1011 time to fit residues: 32.6109 Evaluate side-chains 220 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 302 ILE Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 411 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 0.0040 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN B 424 GLN K 309 ASN ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.155487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113810 restraints weight = 13265.406| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.07 r_work: 0.3348 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10414 Z= 0.111 Angle : 0.517 6.682 14134 Z= 0.263 Chirality : 0.042 0.204 1555 Planarity : 0.004 0.049 1835 Dihedral : 8.046 131.686 1512 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.26 % Allowed : 14.27 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1270 helix: 1.86 (0.23), residues: 502 sheet: 0.59 (0.34), residues: 229 loop : -0.81 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 264 TYR 0.009 0.001 TYR B 310 PHE 0.011 0.001 PHE B 92 TRP 0.009 0.001 TRP A 21 HIS 0.004 0.001 HIS K 323 Details of bonding type rmsd covalent geometry : bond 0.00244 (10414) covalent geometry : angle 0.51729 (14134) hydrogen bonds : bond 0.03908 ( 461) hydrogen bonds : angle 4.37601 ( 1362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7438 (m-80) cc_final: 0.7208 (m-80) REVERT: A 411 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8135 (mm-30) REVERT: B 164 MET cc_start: 0.8131 (mmm) cc_final: 0.7908 (tpp) REVERT: K 129 GLU cc_start: 0.8291 (mp0) cc_final: 0.7948 (mp0) REVERT: K 342 ASP cc_start: 0.8063 (t0) cc_final: 0.7779 (t0) REVERT: K 352 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7423 (mp0) REVERT: K 425 GLU cc_start: 0.8709 (pt0) cc_final: 0.8376 (pt0) REVERT: K 429 ILE cc_start: 0.8632 (mt) cc_final: 0.8073 (mt) REVERT: K 432 SER cc_start: 0.8993 (t) cc_final: 0.8524 (p) REVERT: K 433 LEU cc_start: 0.8931 (mt) cc_final: 0.8656 (mp) REVERT: K 454 ASN cc_start: 0.8075 (m-40) cc_final: 0.7761 (m-40) REVERT: K 460 ASP cc_start: 0.7928 (m-30) cc_final: 0.7263 (m-30) outliers start: 25 outliers final: 17 residues processed: 229 average time/residue: 0.0951 time to fit residues: 31.2918 Evaluate side-chains 223 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 101 LYS Chi-restraints excluded: chain K residue 142 GLU Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 302 ILE Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 411 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 0.3980 chunk 86 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 0.0030 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 424 GLN ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 ASN K 513 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.113910 restraints weight = 13263.621| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.06 r_work: 0.3352 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10414 Z= 0.113 Angle : 0.518 6.709 14134 Z= 0.261 Chirality : 0.042 0.212 1555 Planarity : 0.004 0.048 1835 Dihedral : 7.704 127.437 1512 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.07 % Allowed : 14.18 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.24), residues: 1270 helix: 1.97 (0.23), residues: 502 sheet: 0.71 (0.35), residues: 228 loop : -0.79 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 329 TYR 0.012 0.001 TYR K 308 PHE 0.011 0.001 PHE A 67 TRP 0.009 0.001 TRP A 21 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00252 (10414) covalent geometry : angle 0.51759 (14134) hydrogen bonds : bond 0.03714 ( 461) hydrogen bonds : angle 4.24456 ( 1362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 ASN cc_start: 0.8440 (p0) cc_final: 0.7914 (p0) REVERT: K 342 ASP cc_start: 0.8153 (t0) cc_final: 0.7824 (t0) REVERT: K 415 LYS cc_start: 0.6715 (tmtt) cc_final: 0.6295 (tmmt) REVERT: K 429 ILE cc_start: 0.8628 (mt) cc_final: 0.8032 (mt) REVERT: K 432 SER cc_start: 0.8977 (t) cc_final: 0.8518 (p) REVERT: K 433 LEU cc_start: 0.8890 (mt) cc_final: 0.8612 (mp) REVERT: K 454 ASN cc_start: 0.8133 (m-40) cc_final: 0.7818 (m-40) REVERT: K 502 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7430 (mm) outliers start: 34 outliers final: 25 residues processed: 216 average time/residue: 0.0977 time to fit residues: 30.0487 Evaluate side-chains 223 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 101 LYS Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 302 ILE Chi-restraints excluded: chain K residue 372 MET Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 502 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** K 417 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 = 0.4003 r_free = 0.4003 target = 0.154037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113036 restraints weight = 13219.946| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.98 r_work: 0.3311 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10414 Z= 0.180 Angle : 0.554 6.842 14134 Z= 0.280 Chirality : 0.044 0.206 1555 Planarity : 0.004 0.047 1835 Dihedral : 7.783 128.731 1512 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.43 % Allowed : 14.81 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1270 helix: 1.97 (0.23), residues: 499 sheet: 0.67 (0.35), residues: 229 loop : -0.81 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 413 TYR 0.009 0.001 TYR B 310 PHE 0.018 0.002 PHE A 67 TRP 0.008 0.001 TRP A 21 HIS 0.008 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00432 (10414) covalent geometry : angle 0.55411 (14134) hydrogen bonds : bond 0.04364 ( 461) hydrogen bonds : angle 4.29630 ( 1362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 364 ASN cc_start: 0.8174 (t0) cc_final: 0.7938 (t0) REVERT: K 429 ILE cc_start: 0.8700 (mt) cc_final: 0.8115 (mt) REVERT: K 432 SER cc_start: 0.8993 (t) cc_final: 0.8531 (p) REVERT: K 433 LEU cc_start: 0.8934 (mt) cc_final: 0.8664 (mp) REVERT: K 454 ASN cc_start: 0.8213 (m-40) cc_final: 0.7904 (m-40) REVERT: K 460 ASP cc_start: 0.7960 (m-30) cc_final: 0.7222 (m-30) REVERT: K 502 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7430 (mm) outliers start: 38 outliers final: 31 residues processed: 223 average time/residue: 0.0947 time to fit residues: 30.5707 Evaluate side-chains 237 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 101 LYS Chi-restraints excluded: chain K residue 142 GLU Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 302 ILE Chi-restraints excluded: chain K residue 372 MET Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 411 SER Chi-restraints excluded: chain K residue 502 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 106 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 0.0870 chunk 78 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS K 309 ASN ** K 417 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 = 0.4033 r_free = 0.4033 target = 0.156317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115004 restraints weight = 13409.497| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.12 r_work: 0.3343 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10414 Z= 0.108 Angle : 0.510 6.748 14134 Z= 0.258 Chirality : 0.042 0.209 1555 Planarity : 0.004 0.046 1835 Dihedral : 7.441 125.218 1512 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.80 % Allowed : 15.54 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.24), residues: 1270 helix: 2.03 (0.23), residues: 503 sheet: 0.80 (0.35), residues: 228 loop : -0.90 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 329 TYR 0.008 0.001 TYR B 310 PHE 0.013 0.001 PHE B 92 TRP 0.009 0.001 TRP A 21 HIS 0.003 0.001 HIS K 323 Details of bonding type rmsd covalent geometry : bond 0.00243 (10414) covalent geometry : angle 0.51032 (14134) hydrogen bonds : bond 0.03535 ( 461) hydrogen bonds : angle 4.18385 ( 1362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 PHE cc_start: 0.8750 (m-80) cc_final: 0.8447 (m-80) REVERT: K 73 PHE cc_start: 0.7288 (m-80) cc_final: 0.6910 (m-80) REVERT: K 77 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7151 (mm-30) REVERT: K 369 SER cc_start: 0.7354 (m) cc_final: 0.7026 (t) REVERT: K 415 LYS cc_start: 0.6473 (tmtt) cc_final: 0.5896 (tmmt) REVERT: K 429 ILE cc_start: 0.8683 (mt) cc_final: 0.8079 (mt) REVERT: K 432 SER cc_start: 0.8969 (t) cc_final: 0.8518 (p) REVERT: K 433 LEU cc_start: 0.8907 (mt) cc_final: 0.8627 (mp) REVERT: K 454 ASN cc_start: 0.8202 (m-40) cc_final: 0.7905 (m-40) REVERT: K 502 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7425 (mm) outliers start: 31 outliers final: 24 residues processed: 222 average time/residue: 0.0970 time to fit residues: 30.6564 Evaluate side-chains 222 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 101 LYS Chi-restraints excluded: chain K residue 142 GLU Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 302 ILE Chi-restraints excluded: chain K residue 372 MET Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 502 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 124 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 113 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS K 152 ASN ** K 193 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 = 0.4023 r_free = 0.4023 target = 0.155556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114648 restraints weight = 13249.347| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.00 r_work: 0.3344 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10414 Z= 0.126 Angle : 0.529 7.495 14134 Z= 0.265 Chirality : 0.043 0.214 1555 Planarity : 0.004 0.046 1835 Dihedral : 7.390 124.494 1512 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.71 % Allowed : 15.90 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1270 helix: 2.14 (0.23), residues: 501 sheet: 0.78 (0.35), residues: 229 loop : -0.87 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 329 TYR 0.009 0.001 TYR B 310 PHE 0.015 0.001 PHE B 92 TRP 0.009 0.001 TRP A 21 HIS 0.005 0.001 HIS K 416 Details of bonding type rmsd covalent geometry : bond 0.00291 (10414) covalent geometry : angle 0.52852 (14134) hydrogen bonds : bond 0.03763 ( 461) hydrogen bonds : angle 4.15671 ( 1362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: K 77 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7224 (mm-30) REVERT: K 172 THR cc_start: 0.8019 (m) cc_final: 0.7735 (p) REVERT: K 221 MET cc_start: 0.7856 (mtm) cc_final: 0.7644 (mtm) REVERT: K 364 ASN cc_start: 0.8127 (t0) cc_final: 0.7924 (t0) REVERT: K 369 SER cc_start: 0.7376 (m) cc_final: 0.7048 (t) REVERT: K 429 ILE cc_start: 0.8687 (mt) cc_final: 0.8142 (mt) REVERT: K 432 SER cc_start: 0.8962 (t) cc_final: 0.8504 (p) REVERT: K 433 LEU cc_start: 0.8901 (mt) cc_final: 0.8641 (mt) REVERT: K 454 ASN cc_start: 0.8200 (m-40) cc_final: 0.7908 (m-40) REVERT: K 502 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7413 (mm) outliers start: 30 outliers final: 25 residues processed: 222 average time/residue: 0.0953 time to fit residues: 30.6413 Evaluate side-chains 226 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 142 GLU Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 302 ILE Chi-restraints excluded: chain K residue 307 ILE Chi-restraints excluded: chain K residue 372 MET Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 502 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 116 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS K 152 ASN K 193 GLN ** K 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.152363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111228 restraints weight = 13271.346| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.02 r_work: 0.3285 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10414 Z= 0.223 Angle : 0.598 7.347 14134 Z= 0.303 Chirality : 0.046 0.220 1555 Planarity : 0.004 0.048 1835 Dihedral : 7.813 129.907 1512 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.07 % Allowed : 15.63 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1270 helix: 1.92 (0.23), residues: 504 sheet: 0.84 (0.35), residues: 217 loop : -0.91 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 111 TYR 0.016 0.002 TYR K 308 PHE 0.022 0.002 PHE B 92 TRP 0.007 0.001 TRP A 21 HIS 0.010 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00540 (10414) covalent geometry : angle 0.59819 (14134) hydrogen bonds : bond 0.04822 ( 461) hydrogen bonds : angle 4.31569 ( 1362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8035 (p0) cc_final: 0.7834 (p0) REVERT: B 423 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7842 (tp40) REVERT: K 172 THR cc_start: 0.8046 (m) cc_final: 0.7773 (p) REVERT: K 308 TYR cc_start: 0.8502 (t80) cc_final: 0.8206 (t80) REVERT: K 331 CYS cc_start: 0.8337 (m) cc_final: 0.8055 (m) REVERT: K 364 ASN cc_start: 0.8293 (t0) cc_final: 0.8061 (t0) REVERT: K 369 SER cc_start: 0.7472 (m) cc_final: 0.7119 (t) REVERT: K 429 ILE cc_start: 0.8733 (mt) cc_final: 0.8171 (mt) REVERT: K 432 SER cc_start: 0.8993 (t) cc_final: 0.8545 (p) REVERT: K 433 LEU cc_start: 0.8960 (mt) cc_final: 0.8691 (mt) REVERT: K 454 ASN cc_start: 0.8270 (m-40) cc_final: 0.7968 (m-40) REVERT: K 470 PHE cc_start: 0.8191 (m-80) cc_final: 0.7931 (m-80) REVERT: K 502 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7466 (mm) outliers start: 34 outliers final: 28 residues processed: 234 average time/residue: 0.0991 time to fit residues: 33.1921 Evaluate side-chains 237 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 142 GLU Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 302 ILE Chi-restraints excluded: chain K residue 307 ILE Chi-restraints excluded: chain K residue 372 MET Chi-restraints excluded: chain K residue 385 ILE Chi-restraints excluded: chain K residue 502 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 53 optimal weight: 0.0870 chunk 124 optimal weight: 6.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS K 309 ASN ** K 417 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 = 0.4021 r_free = 0.4021 target = 0.155794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114835 restraints weight = 13231.875| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.07 r_work: 0.3338 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10414 Z= 0.114 Angle : 0.530 6.752 14134 Z= 0.268 Chirality : 0.043 0.220 1555 Planarity : 0.004 0.047 1835 Dihedral : 7.212 127.335 1512 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.71 % Allowed : 16.53 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1270 helix: 2.04 (0.23), residues: 503 sheet: 0.82 (0.34), residues: 227 loop : -0.88 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 413 TYR 0.016 0.001 TYR K 308 PHE 0.018 0.001 PHE B 92 TRP 0.010 0.001 TRP A 21 HIS 0.003 0.001 HIS K 323 Details of bonding type rmsd covalent geometry : bond 0.00253 (10414) covalent geometry : angle 0.52996 (14134) hydrogen bonds : bond 0.03670 ( 461) hydrogen bonds : angle 4.20144 ( 1362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: K 73 PHE cc_start: 0.7286 (m-80) cc_final: 0.6976 (m-80) REVERT: K 80 ARG cc_start: 0.5765 (mtm-85) cc_final: 0.5546 (mtm-85) REVERT: K 172 THR cc_start: 0.8030 (m) cc_final: 0.7778 (p) REVERT: K 329 ARG cc_start: 0.7251 (ttm-80) cc_final: 0.6993 (ttm170) REVERT: K 331 CYS cc_start: 0.8290 (m) cc_final: 0.8007 (m) REVERT: K 364 ASN cc_start: 0.8273 (t0) cc_final: 0.8063 (t0) REVERT: K 369 SER cc_start: 0.7458 (m) cc_final: 0.7166 (p) REVERT: K 429 ILE cc_start: 0.8689 (mt) cc_final: 0.8084 (mt) REVERT: K 432 SER cc_start: 0.8960 (t) cc_final: 0.8502 (p) REVERT: K 433 LEU cc_start: 0.8919 (mt) cc_final: 0.8641 (mt) REVERT: K 454 ASN cc_start: 0.8283 (m-40) cc_final: 0.8001 (m-40) outliers start: 30 outliers final: 24 residues processed: 217 average time/residue: 0.0971 time to fit residues: 30.0261 Evaluate side-chains 224 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 142 GLU Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 302 ILE Chi-restraints excluded: chain K residue 307 ILE Chi-restraints excluded: chain K residue 372 MET Chi-restraints excluded: chain K residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 11 optimal weight: 0.0170 chunk 50 optimal weight: 0.0370 chunk 64 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 37 HIS ** K 417 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 = 0.4028 r_free = 0.4028 target = 0.156398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115327 restraints weight = 13132.826| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.06 r_work: 0.3345 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10414 Z= 0.115 Angle : 0.538 7.510 14134 Z= 0.270 Chirality : 0.043 0.225 1555 Planarity : 0.004 0.046 1835 Dihedral : 6.946 124.589 1512 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.26 % Allowed : 17.34 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1270 helix: 2.09 (0.23), residues: 503 sheet: 0.83 (0.34), residues: 227 loop : -0.85 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 329 TYR 0.018 0.001 TYR K 308 PHE 0.021 0.001 PHE K 136 TRP 0.009 0.001 TRP A 21 HIS 0.003 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00258 (10414) covalent geometry : angle 0.53808 (14134) hydrogen bonds : bond 0.03622 ( 461) hydrogen bonds : angle 4.12475 ( 1362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: B 73 MET cc_start: 0.5455 (ttm) cc_final: 0.5182 (ttm) REVERT: K 73 PHE cc_start: 0.7243 (m-80) cc_final: 0.6974 (m-80) REVERT: K 80 ARG cc_start: 0.5781 (mtm-85) cc_final: 0.5549 (mtm-85) REVERT: K 172 THR cc_start: 0.8048 (m) cc_final: 0.7785 (p) REVERT: K 308 TYR cc_start: 0.8572 (t80) cc_final: 0.8270 (t80) REVERT: K 329 ARG cc_start: 0.7237 (ttm-80) cc_final: 0.6976 (ttm170) REVERT: K 331 CYS cc_start: 0.8266 (m) cc_final: 0.7979 (m) REVERT: K 364 ASN cc_start: 0.8298 (t0) cc_final: 0.8078 (t0) REVERT: K 369 SER cc_start: 0.7462 (m) cc_final: 0.7174 (p) REVERT: K 429 ILE cc_start: 0.8690 (mt) cc_final: 0.8137 (mt) REVERT: K 432 SER cc_start: 0.8948 (t) cc_final: 0.8491 (p) REVERT: K 433 LEU cc_start: 0.8894 (mt) cc_final: 0.8622 (mt) REVERT: K 454 ASN cc_start: 0.8265 (m-40) cc_final: 0.7981 (m-40) outliers start: 25 outliers final: 24 residues processed: 218 average time/residue: 0.0989 time to fit residues: 30.8064 Evaluate side-chains 229 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 143 MET Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 302 ILE Chi-restraints excluded: chain K residue 307 ILE Chi-restraints excluded: chain K residue 372 MET Chi-restraints excluded: chain K residue 385 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 116 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** K 417 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 = 0.4014 r_free = 0.4014 target = 0.155085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113733 restraints weight = 13239.328| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.07 r_work: 0.3344 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 10414 Z= 0.183 Angle : 0.831 59.191 14134 Z= 0.482 Chirality : 0.045 0.502 1555 Planarity : 0.004 0.078 1835 Dihedral : 6.962 124.561 1512 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.44 % Allowed : 17.34 % Favored : 80.22 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1270 helix: 2.09 (0.23), residues: 503 sheet: 0.77 (0.34), residues: 227 loop : -0.84 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 413 TYR 0.027 0.001 TYR A 357 PHE 0.020 0.001 PHE K 136 TRP 0.010 0.001 TRP A 388 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00352 (10414) covalent geometry : angle 0.83093 (14134) hydrogen bonds : bond 0.03817 ( 461) hydrogen bonds : angle 4.17221 ( 1362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2916.63 seconds wall clock time: 50 minutes 40.01 seconds (3040.01 seconds total)