Starting phenix.real_space_refine on Tue Jul 29 07:30:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ag4_15415/07_2025/8ag4_15415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ag4_15415/07_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_15415/07_2025/8ag4_15415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ag4_15415/07_2025/8ag4_15415.map" model { file = "/net/cci-nas-00/data/ceres_data/8ag4_15415/07_2025/8ag4_15415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ag4_15415/07_2025/8ag4_15415.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.57, per 1000 atoms: 0.68 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: 2.77 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.45 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: 3.66 Time building geometry restraints manager: 3.31 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: 9.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 29.920 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), 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 TRP 0.008 0.001 TRP B 247 HIS 0.006 0.001 HIS D 220 PHE 0.018 0.001 PHE B 409 TYR 0.025 0.001 TYR A 103 ARG 0.002 0.000 ARG B 354 Details of bonding type rmsd hydrogen bonds : bond 0.14162 ( 471) hydrogen bonds : angle 6.10048 ( 1287) covalent geometry : bond 0.00334 (11381) covalent geometry : angle 0.49111 (15368) *********************** 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 : 1.367 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: 1.3841 time to fit residues: 467.4213 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 : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.0770 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.145642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116499 restraints weight = 13905.309| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.97 r_work: 0.3385 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11381 Z= 0.147 Angle : 0.499 6.107 15368 Z= 0.266 Chirality : 0.042 0.136 1722 Planarity : 0.004 0.043 1977 Dihedral : 4.230 18.978 1489 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.51 % Allowed : 7.45 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1372 helix: 2.07 (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 TRP 0.010 0.001 TRP C 265 HIS 0.006 0.001 HIS D 220 PHE 0.019 0.001 PHE B 409 TYR 0.012 0.001 TYR A 103 ARG 0.006 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 471) hydrogen bonds : angle 5.24057 ( 1287) covalent geometry : bond 0.00349 (11381) covalent geometry : angle 0.49936 (15368) *********************** 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 313 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 294 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7542 (m-30) cc_final: 0.7305 (m-30) REVERT: A 250 GLU cc_start: 0.7695 (pp20) cc_final: 0.7382 (pp20) REVERT: A 333 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7693 (mt-10) REVERT: A 516 LYS cc_start: 0.8137 (mptt) cc_final: 0.7891 (mptm) REVERT: B 133 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 141 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7892 (ttp80) outliers start: 19 outliers final: 11 residues processed: 295 average time/residue: 1.3815 time to fit residues: 436.2362 Evaluate side-chains 309 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 298 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 51 LYS 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 2 optimal weight: 0.9990 chunk 40 optimal weight: 0.0370 chunk 118 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 68 optimal weight: 30.0000 chunk 36 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.0040 overall best weight: 0.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.147553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118086 restraints weight = 14028.204| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.04 r_work: 0.3395 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11381 Z= 0.106 Angle : 0.453 5.378 15368 Z= 0.243 Chirality : 0.041 0.136 1722 Planarity : 0.003 0.039 1977 Dihedral : 4.075 18.405 1489 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.67 % Allowed : 9.12 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1372 helix: 2.16 (0.27), residues: 394 sheet: 1.10 (0.32), residues: 259 loop : -0.67 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.016 0.001 PHE B 409 TYR 0.009 0.001 TYR A 103 ARG 0.006 0.000 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 471) hydrogen bonds : angle 5.00517 ( 1287) covalent geometry : bond 0.00241 (11381) covalent geometry : angle 0.45252 (15368) *********************** 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 319 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 298 time to evaluate : 1.649 Fit side-chains REVERT: A 192 ASP cc_start: 0.7542 (m-30) cc_final: 0.7303 (m-30) REVERT: A 333 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 372 GLU cc_start: 0.7931 (tp30) cc_final: 0.7728 (mm-30) REVERT: B 133 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 141 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7886 (ttp80) REVERT: C 210 ARG cc_start: 0.8096 (mmt-90) cc_final: 0.7883 (mmt-90) REVERT: C 259 ASP cc_start: 0.7500 (m-30) cc_final: 0.7217 (m-30) REVERT: C 329 MET cc_start: 0.6297 (mmm) cc_final: 0.5792 (mmm) REVERT: D 321 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8483 (mtpp) outliers start: 21 outliers final: 8 residues processed: 300 average time/residue: 1.7723 time to fit residues: 570.9600 Evaluate side-chains 308 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 299 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 527 GLN 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 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 59 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 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 = 0.3869 r_free = 0.3869 target = 0.143832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115393 restraints weight = 14034.154| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.97 r_work: 0.3348 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 11381 Z= 0.306 Angle : 0.602 8.355 15368 Z= 0.315 Chirality : 0.047 0.152 1722 Planarity : 0.004 0.038 1977 Dihedral : 4.614 18.194 1489 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.90 % Allowed : 10.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1372 helix: 1.73 (0.26), residues: 394 sheet: 0.93 (0.31), residues: 273 loop : -0.82 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 276 HIS 0.008 0.001 HIS B 246 PHE 0.027 0.003 PHE B 409 TYR 0.015 0.002 TYR A 409 ARG 0.005 0.001 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.05938 ( 471) hydrogen bonds : angle 5.29856 ( 1287) covalent geometry : bond 0.00766 (11381) covalent geometry : angle 0.60172 (15368) *********************** 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 330 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 306 time to evaluate : 1.317 Fit side-chains REVERT: A 79 ASP cc_start: 0.7652 (t0) cc_final: 0.7401 (t0) REVERT: A 172 GLU cc_start: 0.7490 (tp30) cc_final: 0.7174 (tp30) REVERT: A 192 ASP cc_start: 0.7601 (m-30) cc_final: 0.7365 (m-30) REVERT: A 333 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 372 GLU cc_start: 0.8206 (tp30) cc_final: 0.8004 (mm-30) REVERT: A 516 LYS cc_start: 0.8142 (mptt) cc_final: 0.7917 (mptm) REVERT: B 133 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 141 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7927 (ttp80) REVERT: B 457 LEU cc_start: 0.8594 (tp) cc_final: 0.8394 (tp) REVERT: C 329 MET cc_start: 0.6413 (mmm) cc_final: 0.5812 (mmm) outliers start: 24 outliers final: 14 residues processed: 311 average time/residue: 1.4250 time to fit residues: 473.7740 Evaluate side-chains 313 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 299 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 20 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 152 ASN A 163 HIS A 278 GLN B 6 ASN B 22 ASN B 43 GLN B 50 ASN B 119 GLN B 269 GLN B 352 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117576 restraints weight = 13952.144| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.95 r_work: 0.3371 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11381 Z= 0.163 Angle : 0.504 6.439 15368 Z= 0.269 Chirality : 0.042 0.146 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.425 17.862 1489 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.74 % Allowed : 11.97 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1372 helix: 1.93 (0.27), residues: 394 sheet: 0.94 (0.32), residues: 272 loop : -0.76 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.006 0.001 HIS D 220 PHE 0.021 0.001 PHE B 409 TYR 0.009 0.001 TYR A 71 ARG 0.007 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 471) hydrogen bonds : angle 5.06410 ( 1287) covalent geometry : bond 0.00395 (11381) covalent geometry : angle 0.50393 (15368) *********************** 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 316 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 294 time to evaluate : 1.335 Fit side-chains REVERT: A 172 GLU cc_start: 0.7454 (tp30) cc_final: 0.7119 (tp30) REVERT: A 192 ASP cc_start: 0.7583 (m-30) cc_final: 0.7343 (m-30) REVERT: A 333 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7718 (mt-10) REVERT: B 133 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 141 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7882 (ttp80) REVERT: C 329 MET cc_start: 0.6413 (mmm) cc_final: 0.5798 (mmm) outliers start: 22 outliers final: 17 residues processed: 298 average time/residue: 1.4551 time to fit residues: 463.6468 Evaluate side-chains 307 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 290 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 20 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 481 LYS 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 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 128 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 6 ASN B 22 ASN B 50 ASN B 119 GLN B 269 GLN B 352 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115039 restraints weight = 14093.241| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.04 r_work: 0.3344 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11381 Z= 0.271 Angle : 0.578 7.594 15368 Z= 0.304 Chirality : 0.046 0.157 1722 Planarity : 0.004 0.037 1977 Dihedral : 4.622 17.907 1489 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.46 % Allowed : 12.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1372 helix: 1.71 (0.26), residues: 394 sheet: 0.91 (0.31), residues: 273 loop : -0.86 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 247 HIS 0.007 0.001 HIS B 246 PHE 0.026 0.002 PHE B 409 TYR 0.014 0.002 TYR A 71 ARG 0.005 0.001 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.05574 ( 471) hydrogen bonds : angle 5.19260 ( 1287) covalent geometry : bond 0.00679 (11381) covalent geometry : angle 0.57846 (15368) *********************** 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 327 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 1.202 Fit side-chains REVERT: A 91 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6675 (mm-30) REVERT: A 172 GLU cc_start: 0.7500 (tp30) cc_final: 0.7138 (tp30) REVERT: A 192 ASP cc_start: 0.7613 (m-30) cc_final: 0.7373 (m-30) REVERT: A 333 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 516 LYS cc_start: 0.8128 (mptt) cc_final: 0.7900 (mptm) REVERT: B 133 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8187 (mt-10) REVERT: B 141 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7938 (ttp80) REVERT: C 210 ARG cc_start: 0.8130 (mmt-90) cc_final: 0.7751 (mmt-90) REVERT: C 329 MET cc_start: 0.6422 (mmm) cc_final: 0.5776 (mmm) outliers start: 31 outliers final: 25 residues processed: 306 average time/residue: 1.3269 time to fit residues: 434.8360 Evaluate side-chains 321 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 295 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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 331 LYS Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 481 LYS 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 232 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 97 optimal weight: 0.0870 chunk 53 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 163 HIS A 278 GLN B 6 ASN B 22 ASN B 50 ASN B 119 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.145891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.117556 restraints weight = 14142.878| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.99 r_work: 0.3379 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1400 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= 0.124 Angle : 0.488 5.635 15368 Z= 0.262 Chirality : 0.041 0.149 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.349 17.707 1489 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.90 % Allowed : 13.40 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.23), residues: 1372 helix: 2.06 (0.27), residues: 394 sheet: 1.03 (0.32), residues: 258 loop : -0.79 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.018 0.001 PHE B 409 TYR 0.008 0.001 TYR A 71 ARG 0.008 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 471) hydrogen bonds : angle 4.96014 ( 1287) covalent geometry : bond 0.00292 (11381) covalent geometry : angle 0.48772 (15368) *********************** 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 315 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 291 time to evaluate : 2.119 Fit side-chains REVERT: A 91 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6578 (mm-30) REVERT: A 172 GLU cc_start: 0.7433 (tp30) cc_final: 0.7091 (tp30) REVERT: A 192 ASP cc_start: 0.7615 (m-30) cc_final: 0.7404 (m-30) REVERT: A 333 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 133 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8094 (mt-10) REVERT: B 141 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7864 (ttp80) REVERT: C 210 ARG cc_start: 0.8128 (mmt-90) cc_final: 0.7771 (mmt-90) REVERT: C 329 MET cc_start: 0.6402 (mmm) cc_final: 0.5740 (mmm) outliers start: 24 outliers final: 14 residues processed: 297 average time/residue: 1.7772 time to fit residues: 566.4778 Evaluate side-chains 304 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 289 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 TYR 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 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 293 LEU Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.6980 chunk 118 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 58 optimal weight: 0.0040 chunk 122 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6632 ------------------------------------------------------------------------------- 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 163 HIS A 278 GLN B 6 ASN B 22 ASN B 43 GLN B 119 GLN B 352 GLN ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.146333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117461 restraints weight = 14140.715| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.96 r_work: 0.3386 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11381 Z= 0.142 Angle : 0.498 6.371 15368 Z= 0.264 Chirality : 0.042 0.146 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.326 17.639 1489 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.59 % Allowed : 13.80 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1372 helix: 2.08 (0.27), residues: 394 sheet: 1.04 (0.32), residues: 258 loop : -0.79 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.019 0.001 PHE B 409 TYR 0.009 0.001 TYR A 71 ARG 0.004 0.000 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 471) hydrogen bonds : angle 4.94016 ( 1287) covalent geometry : bond 0.00340 (11381) covalent geometry : angle 0.49768 (15368) *********************** 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 320 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 2.450 Fit side-chains REVERT: A 91 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6566 (mm-30) REVERT: A 172 GLU cc_start: 0.7404 (tp30) cc_final: 0.7084 (tp30) REVERT: A 333 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7660 (mt-10) REVERT: B 133 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8078 (mt-10) REVERT: B 141 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7849 (ttp80) REVERT: C 210 ARG cc_start: 0.8120 (mmt-90) cc_final: 0.7734 (mmt-90) REVERT: C 329 MET cc_start: 0.6365 (mmm) cc_final: 0.5717 (mmm) outliers start: 20 outliers final: 14 residues processed: 306 average time/residue: 1.6780 time to fit residues: 547.0934 Evaluate side-chains 305 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 290 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 461 LYS 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 192 THR Chi-restraints excluded: chain C residue 267 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 93 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 0.0020 chunk 102 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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 6 ASN B 22 ASN B 43 GLN B 119 GLN B 352 GLN ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.147137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117985 restraints weight = 14083.180| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.04 r_work: 0.3394 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11381 Z= 0.105 Angle : 0.477 6.655 15368 Z= 0.253 Chirality : 0.041 0.141 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.174 17.624 1489 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.35 % Allowed : 14.75 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1372 helix: 2.19 (0.27), residues: 394 sheet: 1.05 (0.32), residues: 258 loop : -0.72 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.016 0.001 PHE B 409 TYR 0.007 0.001 TYR A 88 ARG 0.005 0.000 ARG A 258 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 471) hydrogen bonds : angle 4.81743 ( 1287) covalent geometry : bond 0.00239 (11381) covalent geometry : angle 0.47702 (15368) *********************** 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 306 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 289 time to evaluate : 1.253 Fit side-chains REVERT: A 91 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: A 172 GLU cc_start: 0.7394 (tp30) cc_final: 0.7066 (tp30) REVERT: A 329 LEU cc_start: 0.8212 (mp) cc_final: 0.7951 (mt) REVERT: A 333 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 516 LYS cc_start: 0.8094 (mptt) cc_final: 0.7863 (mptm) REVERT: B 133 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 142 PHE cc_start: 0.8693 (p90) cc_final: 0.8397 (p90) REVERT: B 417 GLU cc_start: 0.8660 (pt0) cc_final: 0.8388 (pt0) REVERT: C 179 THR cc_start: 0.8223 (m) cc_final: 0.7848 (p) REVERT: C 210 ARG cc_start: 0.8116 (mmt-90) cc_final: 0.7746 (mmt-90) REVERT: C 329 MET cc_start: 0.6350 (mmm) cc_final: 0.5692 (mmm) outliers start: 17 outliers final: 13 residues processed: 294 average time/residue: 1.4647 time to fit residues: 464.4421 Evaluate side-chains 304 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 290 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 267 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 ASN B 22 ASN B 43 GLN B 119 GLN B 352 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.146234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.117196 restraints weight = 14043.758| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.99 r_work: 0.3387 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1528 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= 0.148 Angle : 0.513 6.845 15368 Z= 0.269 Chirality : 0.042 0.143 1722 Planarity : 0.003 0.036 1977 Dihedral : 4.271 17.688 1489 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.90 % Allowed : 14.99 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1372 helix: 2.13 (0.26), residues: 394 sheet: 1.07 (0.32), residues: 258 loop : -0.74 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.019 0.001 PHE B 409 TYR 0.008 0.001 TYR A 71 ARG 0.009 0.001 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 471) hydrogen bonds : angle 4.89180 ( 1287) covalent geometry : bond 0.00357 (11381) covalent geometry : angle 0.51325 (15368) ********************** 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 317 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 293 time to evaluate : 1.261 Fit side-chains REVERT: A 91 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6532 (mm-30) REVERT: A 172 GLU cc_start: 0.7377 (tp30) cc_final: 0.7101 (tp30) REVERT: A 333 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7635 (mt-10) REVERT: A 516 LYS cc_start: 0.8084 (mptt) cc_final: 0.7870 (mptm) REVERT: B 133 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8045 (mt-10) REVERT: B 142 PHE cc_start: 0.8734 (p90) cc_final: 0.8446 (p90) REVERT: B 210 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8344 (tmm) REVERT: B 417 GLU cc_start: 0.8641 (pt0) cc_final: 0.8382 (pt0) REVERT: C 179 THR cc_start: 0.8267 (m) cc_final: 0.7918 (p) REVERT: C 210 ARG cc_start: 0.8135 (mmt-90) cc_final: 0.7785 (mmt-90) REVERT: C 329 MET cc_start: 0.6395 (mmm) cc_final: 0.5758 (mmm) outliers start: 24 outliers final: 17 residues processed: 300 average time/residue: 1.5464 time to fit residues: 495.1209 Evaluate side-chains 312 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 293 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 281 LEU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 231 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 85 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 163 HIS ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 ASN B 22 ASN B 43 GLN B 119 GLN B 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117603 restraints weight = 14050.821| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.01 r_work: 0.3384 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11381 Z= 0.132 Angle : 0.501 7.649 15368 Z= 0.264 Chirality : 0.042 0.143 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.246 17.635 1489 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.59 % Allowed : 14.91 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1372 helix: 2.15 (0.26), residues: 394 sheet: 1.07 (0.32), residues: 258 loop : -0.72 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.019 0.001 PHE B 409 TYR 0.008 0.001 TYR A 103 ARG 0.007 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 471) hydrogen bonds : angle 4.87201 ( 1287) covalent geometry : bond 0.00314 (11381) covalent geometry : angle 0.50089 (15368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13190.64 seconds wall clock time: 233 minutes 32.70 seconds (14012.70 seconds total)