Starting phenix.real_space_refine on Sat Aug 23 09:26:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ag4_15415/08_2025/8ag4_15415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ag4_15415/08_2025/8ag4_15415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ag4_15415/08_2025/8ag4_15415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ag4_15415/08_2025/8ag4_15415.map" model { file = "/net/cci-nas-00/data/ceres_data/8ag4_15415/08_2025/8ag4_15415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ag4_15415/08_2025/8ag4_15415.cif" } resolution = 2.46 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 7118 2.51 5 N 1861 2.21 5 O 2120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11155 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4054 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 27, 'TRANS': 474} Chain: "B" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4302 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 25, 'TRANS': 513} Chain breaks: 2 Chain: "C" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1412 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1387 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 165} Time building chain proxies: 2.80, per 1000 atoms: 0.25 Number of scatterers: 11155 At special positions: 0 Unit cell: (114.395, 119.405, 112.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2120 8.00 N 1861 7.00 C 7118 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: 1.11 Conformation dependent library (CDL) restraints added in 343.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 14 sheets defined 33.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.582A pdb=" N GLU A 50 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 78 Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.606A pdb=" N ILE A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.770A pdb=" N THR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.681A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 495 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 29 through 49 Processing helix chain 'B' and resid 87 through 97 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.657A pdb=" N LEU B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 231' Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.597A pdb=" N PHE B 355 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 466 through 470 removed outlier: 3.758A pdb=" N LYS B 469 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 470 " --> pdb=" O ASP B 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 466 through 470' Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.538A pdb=" N LYS B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.160A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.504A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 4.069A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS B 525 " --> pdb=" O GLU B 521 " (cutoff:3.500A) Proline residue: B 529 - end of helix removed outlier: 3.720A pdb=" N THR B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 536 " --> pdb=" O LYS B 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 246 through 251 removed outlier: 4.372A pdb=" N GLU C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 298 removed outlier: 3.790A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.548A pdb=" N LYS D 227 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 243 Processing helix chain 'D' and resid 281 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 6.643A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLU A 107 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU A 83 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 262 removed outlier: 7.928A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR A 401 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU A 345 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS A 260 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU A 347 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LYS A 262 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY A 349 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 304 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.186A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N TYR B 225 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.572A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AB2, first strand: chain 'C' and resid 165 through 168 Processing sheet with id=AB3, first strand: chain 'C' and resid 231 through 232 removed outlier: 6.695A pdb=" N GLY C 205 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AB5, first strand: chain 'D' and resid 231 through 232 removed outlier: 6.468A pdb=" N GLY D 205 " --> pdb=" O VAL D 217 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1287 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: 1.81 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3638 1.34 - 1.46: 1744 1.46 - 1.57: 5908 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 11381 Sorted by residual: bond pdb=" C THR B 524 " pdb=" O THR B 524 " ideal model delta sigma weight residual 1.237 1.250 -0.014 1.19e-02 7.06e+03 1.35e+00 bond pdb=" CA ILE B 528 " pdb=" C ILE B 528 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.05e-02 9.07e+03 1.03e+00 bond pdb=" CA ASN B 66 " pdb=" CB ASN B 66 " ideal model delta sigma weight residual 1.534 1.546 -0.013 1.30e-02 5.92e+03 9.65e-01 bond pdb=" C ASN D 328 " pdb=" N MET D 329 " ideal model delta sigma weight residual 1.331 1.351 -0.020 2.07e-02 2.33e+03 9.26e-01 bond pdb=" CG1 ILE A 116 " pdb=" CD1 ILE A 116 " ideal model delta sigma weight residual 1.513 1.478 0.035 3.90e-02 6.57e+02 7.99e-01 ... (remaining 11376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 15175 1.80 - 3.60: 173 3.60 - 5.40: 18 5.40 - 7.20: 1 7.20 - 9.00: 1 Bond angle restraints: 15368 Sorted by residual: angle pdb=" N MET B 20 " pdb=" CA MET B 20 " pdb=" C MET B 20 " ideal model delta sigma weight residual 111.81 107.81 4.00 1.44e+00 4.82e-01 7.72e+00 angle pdb=" C GLN B 527 " pdb=" N ILE B 528 " pdb=" CA ILE B 528 " ideal model delta sigma weight residual 122.13 117.09 5.04 1.85e+00 2.92e-01 7.43e+00 angle pdb=" C ASN D 219 " pdb=" N HIS D 220 " pdb=" CA HIS D 220 " ideal model delta sigma weight residual 123.05 126.57 -3.52 1.57e+00 4.06e-01 5.02e+00 angle pdb=" CA LYS A 249 " pdb=" CB LYS A 249 " pdb=" CG LYS A 249 " ideal model delta sigma weight residual 114.10 118.19 -4.09 2.00e+00 2.50e-01 4.18e+00 angle pdb=" C TYR A 217 " pdb=" N ARG A 218 " pdb=" CA ARG A 218 " ideal model delta sigma weight residual 121.54 125.16 -3.62 1.91e+00 2.74e-01 3.59e+00 ... (remaining 15363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6339 17.54 - 35.09: 492 35.09 - 52.63: 89 52.63 - 70.18: 24 70.18 - 87.72: 12 Dihedral angle restraints: 6956 sinusoidal: 2890 harmonic: 4066 Sorted by residual: dihedral pdb=" CA PHE D 246 " pdb=" C PHE D 246 " pdb=" N SER D 247 " pdb=" CA SER D 247 " ideal model delta harmonic sigma weight residual 180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA THR D 242 " pdb=" C THR D 242 " pdb=" N ILE D 243 " pdb=" CA ILE D 243 " ideal model delta harmonic sigma weight residual -180.00 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG B 260 " pdb=" CD ARG B 260 " pdb=" NE ARG B 260 " pdb=" CZ ARG B 260 " ideal model delta sinusoidal sigma weight residual 180.00 135.49 44.51 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 6953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 938 0.027 - 0.053: 483 0.053 - 0.080: 169 0.080 - 0.107: 95 0.107 - 0.134: 37 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA ILE C 319 " pdb=" N ILE C 319 " pdb=" C ILE C 319 " pdb=" CB ILE C 319 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA HIS D 220 " pdb=" N HIS D 220 " pdb=" C HIS D 220 " pdb=" CB HIS D 220 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL B 361 " pdb=" N VAL B 361 " pdb=" C VAL B 361 " pdb=" CB VAL B 361 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1719 not shown) Planarity restraints: 1977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 282 " 0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 283 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " -0.011 2.00e-02 2.50e+03 1.02e-02 2.09e+00 pdb=" CG TYR A 103 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 369 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO A 370 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.020 5.00e-02 4.00e+02 ... (remaining 1974 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 340 2.72 - 3.26: 10367 3.26 - 3.81: 16871 3.81 - 4.35: 22089 4.35 - 4.90: 37223 Nonbonded interactions: 86890 Sorted by model distance: nonbonded pdb=" OH TYR D 169 " pdb=" OD1 ASP D 284 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR B 19 " pdb=" OG SER B 139 " model vdw 2.209 3.040 nonbonded pdb=" NZ LYS A 461 " pdb=" OE1 GLU A 524 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR C 305 " pdb=" OD2 ASP D 259 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN B 66 " pdb=" OG SER B 69 " model vdw 2.228 3.040 ... (remaining 86885 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' and resid 162 through 331) 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: 2.600 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.003 0.035 11381 Z= 0.141 Angle : 0.491 8.999 15368 Z= 0.262 Chirality : 0.041 0.134 1722 Planarity : 0.003 0.059 1977 Dihedral : 13.589 87.722 4314 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.77 (0.23), residues: 1372 helix: 2.18 (0.27), residues: 382 sheet: 1.20 (0.33), residues: 250 loop : -0.66 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.025 0.001 TYR A 103 PHE 0.018 0.001 PHE B 409 TRP 0.008 0.001 TRP B 247 HIS 0.006 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00334 (11381) covalent geometry : angle 0.49111 (15368) hydrogen bonds : bond 0.14162 ( 471) hydrogen bonds : angle 6.10048 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.494 Fit side-chains REVERT: A 333 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 133 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8310 (mt-10) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.6996 time to fit residues: 235.9223 Evaluate side-chains 294 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 163 HIS A 278 GLN B 22 ASN B 50 ASN B 269 GLN B 352 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116977 restraints weight = 14114.507| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.98 r_work: 0.3388 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11381 Z= 0.134 Angle : 0.490 5.772 15368 Z= 0.262 Chirality : 0.042 0.136 1722 Planarity : 0.003 0.042 1977 Dihedral : 4.188 18.994 1489 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.67 % Allowed : 7.45 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.72 (0.23), residues: 1372 helix: 2.10 (0.27), residues: 394 sheet: 1.09 (0.32), residues: 259 loop : -0.71 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 210 TYR 0.013 0.001 TYR A 103 PHE 0.018 0.001 PHE B 409 TRP 0.010 0.001 TRP C 265 HIS 0.006 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00312 (11381) covalent geometry : angle 0.49039 (15368) hydrogen bonds : bond 0.04457 ( 471) hydrogen bonds : angle 5.21241 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 299 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 134 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7342 (ttp) REVERT: A 247 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7582 (mmm160) REVERT: A 250 GLU cc_start: 0.7684 (pp20) cc_final: 0.7356 (pp20) REVERT: A 333 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 516 LYS cc_start: 0.8127 (mptt) cc_final: 0.7875 (mptm) REVERT: B 133 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 141 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7869 (ttp80) outliers start: 21 outliers final: 9 residues processed: 301 average time/residue: 0.6586 time to fit residues: 212.1007 Evaluate side-chains 305 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 295 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 103 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 111 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 278 GLN B 22 ASN B 43 GLN B 50 ASN B 119 GLN B 352 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.145516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116186 restraints weight = 14188.400| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.01 r_work: 0.3377 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11381 Z= 0.152 Angle : 0.486 6.310 15368 Z= 0.259 Chirality : 0.042 0.134 1722 Planarity : 0.003 0.038 1977 Dihedral : 4.233 18.327 1489 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.35 % Allowed : 9.75 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.70 (0.23), residues: 1372 helix: 2.07 (0.27), residues: 394 sheet: 1.10 (0.32), residues: 259 loop : -0.72 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 44 TYR 0.009 0.001 TYR A 217 PHE 0.019 0.001 PHE B 409 TRP 0.009 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00367 (11381) covalent geometry : angle 0.48619 (15368) hydrogen bonds : bond 0.04535 ( 471) hydrogen bonds : angle 5.11168 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 294 time to evaluate : 0.460 Fit side-chains REVERT: A 333 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 133 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8100 (mt-10) REVERT: B 141 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7887 (ttp80) REVERT: B 399 LYS cc_start: 0.8314 (mtpp) cc_final: 0.8108 (ttmm) REVERT: B 534 LYS cc_start: 0.8393 (tttp) cc_final: 0.8160 (tttt) REVERT: C 329 MET cc_start: 0.6320 (mmm) cc_final: 0.5780 (mmm) REVERT: D 321 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8492 (mtpp) outliers start: 17 outliers final: 10 residues processed: 295 average time/residue: 0.5298 time to fit residues: 167.8938 Evaluate side-chains 303 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 292 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 89 optimal weight: 0.0980 chunk 126 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 278 GLN B 22 ASN B 50 ASN B 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.146503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116981 restraints weight = 14071.887| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.03 r_work: 0.3375 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11381 Z= 0.154 Angle : 0.488 6.336 15368 Z= 0.260 Chirality : 0.042 0.134 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.266 17.906 1489 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.98 % Allowed : 10.63 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.70 (0.23), residues: 1372 helix: 2.08 (0.27), residues: 394 sheet: 1.06 (0.32), residues: 260 loop : -0.71 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 130 TYR 0.009 0.001 TYR A 103 PHE 0.020 0.001 PHE B 409 TRP 0.009 0.001 TRP C 265 HIS 0.006 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00374 (11381) covalent geometry : angle 0.48843 (15368) hydrogen bonds : bond 0.04439 ( 471) hydrogen bonds : angle 4.99793 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 290 time to evaluate : 0.346 Fit side-chains REVERT: A 91 GLU cc_start: 0.6820 (mp0) cc_final: 0.6584 (mm-30) REVERT: A 333 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7779 (mt-10) REVERT: B 133 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 141 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7894 (ttp80) REVERT: C 329 MET cc_start: 0.6351 (mmm) cc_final: 0.5847 (mmm) outliers start: 25 outliers final: 13 residues processed: 294 average time/residue: 0.5844 time to fit residues: 183.9766 Evaluate side-chains 303 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 290 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.0170 chunk 31 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 278 GLN B 22 ASN B 50 ASN B 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.145691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116423 restraints weight = 13955.097| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.98 r_work: 0.3378 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11381 Z= 0.178 Angle : 0.506 6.766 15368 Z= 0.268 Chirality : 0.043 0.140 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.362 17.892 1489 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.90 % Allowed : 11.58 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.67 (0.23), residues: 1372 helix: 2.04 (0.27), residues: 394 sheet: 1.05 (0.32), residues: 260 loop : -0.73 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 210 TYR 0.014 0.001 TYR A 103 PHE 0.021 0.002 PHE B 409 TRP 0.010 0.001 TRP B 247 HIS 0.006 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00437 (11381) covalent geometry : angle 0.50602 (15368) hydrogen bonds : bond 0.04674 ( 471) hydrogen bonds : angle 5.00473 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 289 time to evaluate : 0.314 Fit side-chains REVERT: A 333 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7760 (mt-10) REVERT: B 141 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7839 (ttp80) REVERT: C 210 ARG cc_start: 0.8073 (mmt-90) cc_final: 0.7666 (mmt-90) REVERT: C 329 MET cc_start: 0.6396 (mmm) cc_final: 0.5820 (mmm) outliers start: 24 outliers final: 17 residues processed: 292 average time/residue: 0.6122 time to fit residues: 191.3415 Evaluate side-chains 304 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 287 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 132 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 152 ASN A 278 GLN B 22 ASN B 119 GLN B 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.146426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117882 restraints weight = 14178.307| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.99 r_work: 0.3389 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11381 Z= 0.112 Angle : 0.471 6.282 15368 Z= 0.250 Chirality : 0.041 0.142 1722 Planarity : 0.003 0.036 1977 Dihedral : 4.208 19.411 1489 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.67 % Allowed : 12.45 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.77 (0.23), residues: 1372 helix: 2.18 (0.27), residues: 394 sheet: 1.09 (0.32), residues: 258 loop : -0.69 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 210 TYR 0.008 0.001 TYR A 103 PHE 0.017 0.001 PHE B 409 TRP 0.009 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00258 (11381) covalent geometry : angle 0.47108 (15368) hydrogen bonds : bond 0.03931 ( 471) hydrogen bonds : angle 4.87138 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 292 time to evaluate : 0.396 Fit side-chains REVERT: A 333 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 141 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7891 (ttp80) REVERT: C 179 THR cc_start: 0.8236 (m) cc_final: 0.7913 (p) REVERT: C 210 ARG cc_start: 0.8087 (mmt-90) cc_final: 0.7866 (mmt180) REVERT: C 329 MET cc_start: 0.6365 (mmm) cc_final: 0.5822 (mmm) REVERT: D 321 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8493 (mtpp) outliers start: 21 outliers final: 19 residues processed: 296 average time/residue: 0.5758 time to fit residues: 182.2151 Evaluate side-chains 316 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 296 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 121 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 278 GLN B 22 ASN B 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.145926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117360 restraints weight = 14079.660| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.98 r_work: 0.3380 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11381 Z= 0.144 Angle : 0.496 6.454 15368 Z= 0.261 Chirality : 0.042 0.140 1722 Planarity : 0.003 0.036 1977 Dihedral : 4.252 19.831 1489 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.14 % Allowed : 12.69 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.72 (0.23), residues: 1372 helix: 2.11 (0.27), residues: 394 sheet: 1.04 (0.32), residues: 260 loop : -0.69 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 130 TYR 0.010 0.001 TYR A 103 PHE 0.019 0.001 PHE B 409 TRP 0.008 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00345 (11381) covalent geometry : angle 0.49577 (15368) hydrogen bonds : bond 0.04202 ( 471) hydrogen bonds : angle 4.87557 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 283 time to evaluate : 0.414 Fit side-chains REVERT: A 333 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 179 THR cc_start: 0.8240 (m) cc_final: 0.7913 (p) REVERT: C 210 ARG cc_start: 0.8080 (mmt-90) cc_final: 0.7694 (mmt-90) REVERT: C 329 MET cc_start: 0.6423 (mmm) cc_final: 0.5846 (mmm) REVERT: D 321 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8484 (mtpp) outliers start: 27 outliers final: 23 residues processed: 288 average time/residue: 0.6077 time to fit residues: 187.6857 Evaluate side-chains 313 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 289 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 103 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 0.0670 chunk 122 optimal weight: 2.9990 chunk 96 optimal weight: 0.0070 chunk 102 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 278 GLN B 22 ASN B 119 GLN ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118254 restraints weight = 14150.376| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.98 r_work: 0.3394 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11381 Z= 0.109 Angle : 0.474 6.116 15368 Z= 0.251 Chirality : 0.041 0.140 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.171 20.189 1489 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.82 % Allowed : 13.16 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.78 (0.23), residues: 1372 helix: 2.20 (0.27), residues: 394 sheet: 1.09 (0.32), residues: 258 loop : -0.68 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 141 TYR 0.010 0.001 TYR A 103 PHE 0.016 0.001 PHE B 409 TRP 0.009 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00252 (11381) covalent geometry : angle 0.47448 (15368) hydrogen bonds : bond 0.03755 ( 471) hydrogen bonds : angle 4.79712 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 0.327 Fit side-chains REVERT: A 91 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6652 (mm-30) REVERT: A 333 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 142 PHE cc_start: 0.8710 (p90) cc_final: 0.7958 (p90) REVERT: C 179 THR cc_start: 0.8233 (m) cc_final: 0.7894 (p) REVERT: C 210 ARG cc_start: 0.8082 (mmt-90) cc_final: 0.7876 (mmt-90) REVERT: C 329 MET cc_start: 0.6407 (mmm) cc_final: 0.5776 (mmm) outliers start: 23 outliers final: 18 residues processed: 301 average time/residue: 0.5845 time to fit residues: 187.9223 Evaluate side-chains 310 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.0170 chunk 67 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 278 GLN B 22 ASN B 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117198 restraints weight = 13927.699| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.01 r_work: 0.3385 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11381 Z= 0.148 Angle : 0.503 7.575 15368 Z= 0.264 Chirality : 0.042 0.142 1722 Planarity : 0.003 0.039 1977 Dihedral : 4.254 20.323 1489 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.14 % Allowed : 13.40 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.73 (0.23), residues: 1372 helix: 2.12 (0.26), residues: 394 sheet: 1.10 (0.32), residues: 258 loop : -0.71 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 363 TYR 0.008 0.001 TYR A 71 PHE 0.020 0.001 PHE B 409 TRP 0.007 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00357 (11381) covalent geometry : angle 0.50339 (15368) hydrogen bonds : bond 0.04187 ( 471) hydrogen bonds : angle 4.85611 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 0.462 Fit side-chains REVERT: A 91 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6645 (mm-30) REVERT: A 333 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 142 PHE cc_start: 0.8720 (p90) cc_final: 0.8432 (p90) REVERT: B 210 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8423 (tmm) REVERT: C 179 THR cc_start: 0.8234 (m) cc_final: 0.7877 (p) REVERT: C 329 MET cc_start: 0.6402 (mmm) cc_final: 0.5778 (mmm) outliers start: 27 outliers final: 24 residues processed: 297 average time/residue: 0.6194 time to fit residues: 196.5892 Evaluate side-chains 316 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 290 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 80 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 131 optimal weight: 0.0030 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.147385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118050 restraints weight = 14109.810| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.03 r_work: 0.3398 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11381 Z= 0.106 Angle : 0.478 7.464 15368 Z= 0.253 Chirality : 0.041 0.142 1722 Planarity : 0.003 0.045 1977 Dihedral : 4.147 23.200 1489 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.98 % Allowed : 13.56 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.80 (0.23), residues: 1372 helix: 2.24 (0.27), residues: 394 sheet: 1.09 (0.32), residues: 258 loop : -0.68 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 258 TYR 0.007 0.001 TYR B 397 PHE 0.016 0.001 PHE B 409 TRP 0.009 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00242 (11381) covalent geometry : angle 0.47818 (15368) hydrogen bonds : bond 0.03668 ( 471) hydrogen bonds : angle 4.78269 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 288 time to evaluate : 0.374 Fit side-chains REVERT: A 91 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6649 (mm-30) REVERT: A 333 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7731 (mt-10) REVERT: B 142 PHE cc_start: 0.8693 (p90) cc_final: 0.7967 (p90) REVERT: C 179 THR cc_start: 0.8213 (m) cc_final: 0.7849 (p) REVERT: C 329 MET cc_start: 0.6411 (mmm) cc_final: 0.5783 (mmm) outliers start: 25 outliers final: 21 residues processed: 294 average time/residue: 0.5998 time to fit residues: 188.6260 Evaluate side-chains 305 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117380 restraints weight = 14097.141| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.98 r_work: 0.3382 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11381 Z= 0.156 Angle : 0.517 8.164 15368 Z= 0.271 Chirality : 0.042 0.142 1722 Planarity : 0.003 0.042 1977 Dihedral : 4.298 26.933 1489 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.74 % Allowed : 13.96 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 aren not related in a simple way. whole: 0.72 (0.23), residues: 1372 helix: 2.13 (0.26), residues: 394 sheet: 1.08 (0.32), residues: 258 loop : -0.72 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 258 TYR 0.009 0.001 TYR A 103 PHE 0.020 0.001 PHE B 409 TRP 0.007 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00378 (11381) covalent geometry : angle 0.51660 (15368) hydrogen bonds : bond 0.04295 ( 471) hydrogen bonds : angle 4.87096 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5494.56 seconds wall clock time: 93 minutes 54.65 seconds (5634.65 seconds total)