Starting phenix.real_space_refine on Wed Sep 25 20:03:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/09_2024/8ag4_15415.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/09_2024/8ag4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/09_2024/8ag4_15415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/09_2024/8ag4_15415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/09_2024/8ag4_15415.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/09_2024/8ag4_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.89, per 1000 atoms: 0.62 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: 2.97 Conformation dependent library (CDL) restraints added in 1.4 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: 1.33 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: 3.36 Time building geometry restraints manager: 2.97 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: 2.700 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: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.030 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- 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= 0.219 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 1.232 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: 1.3499 time to fit residues: 457.0424 Evaluate side-chains 294 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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= 0.228 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 *********************** 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 fitting. rotamer outliers: 19 poor density : 294 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 250 GLU cc_start: 0.7626 (pp20) cc_final: 0.7343 (pp20) REVERT: A 333 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 516 LYS cc_start: 0.7987 (mptt) cc_final: 0.7782 (mptm) REVERT: B 133 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8238 (mt-10) outliers start: 19 outliers final: 11 residues processed: 295 average time/residue: 1.3472 time to fit residues: 426.3586 Evaluate side-chains 309 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 298 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 69 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 123 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 B 50 ASN B 119 GLN B 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11381 Z= 0.219 Angle : 0.480 6.033 15368 Z= 0.257 Chirality : 0.042 0.134 1722 Planarity : 0.003 0.042 1977 Dihedral : 4.214 18.431 1489 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.67 % Allowed : 9.04 % Favored : 89.29 % 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: 0.71 (0.23), residues: 1372 helix: 2.07 (0.27), residues: 394 sheet: 1.11 (0.32), residues: 259 loop : -0.71 (0.24), residues: 719 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 217 ARG 0.008 0.000 ARG B 141 *********************** 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 316 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 295 time to evaluate : 1.293 Fit side-chains REVERT: A 333 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7773 (mt-10) REVERT: B 133 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8303 (mt-10) REVERT: B 534 LYS cc_start: 0.8356 (tttp) cc_final: 0.8134 (tttt) REVERT: C 329 MET cc_start: 0.6267 (mmm) cc_final: 0.5734 (mmm) outliers start: 21 outliers final: 10 residues processed: 298 average time/residue: 1.3719 time to fit residues: 438.5656 Evaluate side-chains 302 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 292 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 51 LYS Chi-restraints excluded: chain B residue 118 ILE 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 302 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.0370 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11381 Z= 0.251 Angle : 0.488 6.430 15368 Z= 0.259 Chirality : 0.042 0.133 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.265 18.464 1489 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.82 % Allowed : 10.55 % Favored : 87.63 % 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: 0.69 (0.23), residues: 1372 helix: 2.06 (0.27), residues: 394 sheet: 1.08 (0.32), residues: 260 loop : -0.72 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.006 0.001 HIS D 220 PHE 0.020 0.001 PHE B 409 TYR 0.009 0.001 TYR A 217 ARG 0.007 0.000 ARG C 210 *********************** 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 fitting. rotamer outliers: 23 poor density : 292 time to evaluate : 1.252 Fit side-chains REVERT: A 79 ASP cc_start: 0.7376 (t0) cc_final: 0.7152 (t0) REVERT: A 91 GLU cc_start: 0.6755 (mp0) cc_final: 0.6531 (mm-30) REVERT: A 333 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7827 (mt-10) REVERT: B 133 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8320 (mt-10) REVERT: C 329 MET cc_start: 0.6343 (mmm) cc_final: 0.5804 (mmm) outliers start: 23 outliers final: 11 residues processed: 295 average time/residue: 1.3214 time to fit residues: 418.9339 Evaluate side-chains 303 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 292 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 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 110 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 113 optimal weight: 0.0970 chunk 91 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.0010 chunk 118 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 overall best weight: 0.3342 ------------------------------------------------------------------------------- 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 50 ASN B 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1259 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= 0.144 Angle : 0.444 5.344 15368 Z= 0.238 Chirality : 0.040 0.139 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.067 18.084 1489 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.74 % Allowed : 11.50 % Favored : 86.76 % 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: 0.79 (0.24), residues: 1372 helix: 2.23 (0.27), residues: 394 sheet: 1.06 (0.32), residues: 260 loop : -0.68 (0.24), residues: 718 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 0.016 0.001 PHE B 409 TYR 0.008 0.001 TYR A 103 ARG 0.006 0.000 ARG C 210 *********************** 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 319 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 297 time to evaluate : 1.257 Fit side-chains REVERT: A 91 GLU cc_start: 0.6758 (mp0) cc_final: 0.6535 (mm-30) REVERT: A 333 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7806 (mt-10) REVERT: B 133 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8288 (mt-10) REVERT: B 142 PHE cc_start: 0.8759 (p90) cc_final: 0.8044 (p90) REVERT: C 329 MET cc_start: 0.6337 (mmm) cc_final: 0.5804 (mmm) outliers start: 22 outliers final: 15 residues processed: 300 average time/residue: 1.3051 time to fit residues: 421.2491 Evaluate side-chains 308 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 293 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 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 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 240 MET Chi-restraints excluded: chain C residue 267 THR 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 44 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 269 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11381 Z= 0.200 Angle : 0.472 5.837 15368 Z= 0.250 Chirality : 0.041 0.136 1722 Planarity : 0.003 0.036 1977 Dihedral : 4.129 17.561 1489 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.59 % Allowed : 11.97 % Favored : 86.44 % 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: 0.75 (0.23), residues: 1372 helix: 2.18 (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 TRP 0.007 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.018 0.001 PHE B 409 TYR 0.012 0.001 TYR A 103 ARG 0.008 0.000 ARG C 210 *********************** 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 317 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 297 time to evaluate : 1.344 Fit side-chains REVERT: A 91 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6551 (mm-30) REVERT: A 333 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 142 PHE cc_start: 0.8774 (p90) cc_final: 0.8035 (p90) REVERT: C 329 MET cc_start: 0.6416 (mmm) cc_final: 0.5835 (mmm) outliers start: 20 outliers final: 15 residues processed: 302 average time/residue: 1.3516 time to fit residues: 437.3522 Evaluate side-chains 312 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 296 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 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 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 127 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 B 269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11381 Z= 0.329 Angle : 0.530 7.162 15368 Z= 0.279 Chirality : 0.044 0.144 1722 Planarity : 0.003 0.036 1977 Dihedral : 4.362 17.836 1489 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.59 % Allowed : 12.85 % Favored : 85.57 % 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: 0.64 (0.23), residues: 1372 helix: 2.03 (0.26), residues: 393 sheet: 1.06 (0.32), residues: 261 loop : -0.76 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 247 HIS 0.006 0.001 HIS D 220 PHE 0.022 0.002 PHE B 409 TYR 0.011 0.002 TYR A 409 ARG 0.009 0.001 ARG C 210 *********************** 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 318 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 298 time to evaluate : 1.348 Fit side-chains REVERT: A 91 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6489 (mm-30) REVERT: A 333 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 142 PHE cc_start: 0.8819 (p90) cc_final: 0.8590 (p90) REVERT: B 209 LYS cc_start: 0.8645 (mtpm) cc_final: 0.8387 (mtpt) REVERT: C 329 MET cc_start: 0.6414 (mmm) cc_final: 0.5827 (mmm) outliers start: 20 outliers final: 18 residues processed: 304 average time/residue: 1.4082 time to fit residues: 458.1670 Evaluate side-chains 306 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 287 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 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 197 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 240 MET Chi-restraints excluded: chain C residue 267 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 0.0270 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 89 optimal weight: 0.0970 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 overall best weight: 0.5636 ------------------------------------------------------------------------------- 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 269 GLN B 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11381 Z= 0.199 Angle : 0.490 6.308 15368 Z= 0.260 Chirality : 0.041 0.152 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.214 17.709 1489 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.98 % Allowed : 12.69 % Favored : 85.33 % 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: 2.11 (0.27), residues: 394 sheet: 1.02 (0.32), residues: 260 loop : -0.71 (0.24), residues: 718 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 0.018 0.001 PHE B 409 TYR 0.014 0.001 TYR A 103 ARG 0.011 0.001 ARG A 130 *********************** 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 317 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 292 time to evaluate : 1.227 Fit side-chains REVERT: A 91 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6479 (mm-30) REVERT: A 333 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7811 (mt-10) REVERT: B 142 PHE cc_start: 0.8784 (p90) cc_final: 0.8516 (p90) REVERT: C 179 THR cc_start: 0.8277 (m) cc_final: 0.7928 (p) REVERT: C 210 ARG cc_start: 0.8038 (mmt-90) cc_final: 0.7810 (mmt-90) REVERT: C 329 MET cc_start: 0.6405 (mmm) cc_final: 0.5784 (mmm) outliers start: 25 outliers final: 24 residues processed: 300 average time/residue: 1.3229 time to fit residues: 426.0657 Evaluate side-chains 323 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 298 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 20 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.8980 chunk 123 optimal weight: 0.3980 chunk 126 optimal weight: 0.0870 chunk 74 optimal weight: 0.0370 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 0.0040 chunk 37 optimal weight: 0.0070 chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.1066 ------------------------------------------------------------------------------- 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 269 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11381 Z= 0.123 Angle : 0.453 6.819 15368 Z= 0.240 Chirality : 0.040 0.145 1722 Planarity : 0.003 0.041 1977 Dihedral : 3.923 17.360 1489 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.59 % Allowed : 13.24 % 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 (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: 0.85 (0.23), residues: 1372 helix: 2.31 (0.27), residues: 394 sheet: 1.08 (0.33), residues: 253 loop : -0.63 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 247 HIS 0.005 0.000 HIS D 220 PHE 0.014 0.001 PHE B 59 TYR 0.008 0.001 TYR D 306 ARG 0.009 0.000 ARG A 258 *********************** 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 321 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 301 time to evaluate : 1.328 Fit side-chains REVERT: A 333 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7737 (mt-10) REVERT: B 142 PHE cc_start: 0.8706 (p90) cc_final: 0.8005 (p90) REVERT: B 158 ASP cc_start: 0.7599 (t0) cc_final: 0.7115 (t0) REVERT: B 210 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8182 (tmm) REVERT: C 179 THR cc_start: 0.8257 (m) cc_final: 0.7853 (p) REVERT: C 329 MET cc_start: 0.6389 (mmm) cc_final: 0.5785 (mmm) outliers start: 20 outliers final: 12 residues processed: 306 average time/residue: 1.3242 time to fit residues: 434.4410 Evaluate side-chains 302 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 289 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET 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 210 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 167 ILE 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 130 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 43 GLN B 119 GLN B 269 GLN B 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1469 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= 0.221 Angle : 0.499 8.481 15368 Z= 0.261 Chirality : 0.042 0.151 1722 Planarity : 0.003 0.041 1977 Dihedral : 4.111 17.603 1489 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.95 % Allowed : 14.12 % Favored : 84.93 % 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 (0.23), residues: 1372 helix: 2.21 (0.26), residues: 394 sheet: 1.01 (0.32), residues: 260 loop : -0.65 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.018 0.001 PHE B 409 TYR 0.012 0.001 TYR A 103 ARG 0.009 0.001 ARG A 258 ********************** 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 299 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 287 time to evaluate : 1.343 Fit side-chains REVERT: A 333 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7784 (mt-10) REVERT: B 142 PHE cc_start: 0.8774 (p90) cc_final: 0.8045 (p90) REVERT: C 179 THR cc_start: 0.8266 (m) cc_final: 0.7885 (p) REVERT: C 329 MET cc_start: 0.6423 (mmm) cc_final: 0.5791 (mmm) outliers start: 12 outliers final: 10 residues processed: 291 average time/residue: 1.2823 time to fit residues: 400.9071 Evaluate side-chains 298 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 288 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 434 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 167 ILE 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 115 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 B 269 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 = 0.3909 r_free = 0.3909 target = 0.146692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117465 restraints weight = 13907.883| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.99 r_work: 0.3391 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1477 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= 0.217 Angle : 0.504 9.170 15368 Z= 0.263 Chirality : 0.042 0.153 1722 Planarity : 0.003 0.039 1977 Dihedral : 4.144 17.564 1489 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.95 % Allowed : 14.20 % Favored : 84.85 % 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 (0.23), residues: 1372 helix: 2.20 (0.26), residues: 394 sheet: 1.04 (0.32), residues: 260 loop : -0.66 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 265 HIS 0.005 0.001 HIS D 220 PHE 0.018 0.001 PHE B 409 TYR 0.020 0.001 TYR A 103 ARG 0.010 0.001 ARG C 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6539.29 seconds wall clock time: 114 minutes 10.63 seconds (6850.63 seconds total)