Starting phenix.real_space_refine on Wed Jun 26 22:50:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/06_2024/8ag4_15415.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/06_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_15415/06_2024/8ag4_15415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/06_2024/8ag4_15415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/06_2024/8ag4_15415.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/06_2024/8ag4_15415.pdb" } 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 Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "B TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 241": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 6.92, 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 - 3.50 Amino acid : False - 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: 3.97 Conformation dependent library (CDL) restraints added in 2.0 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: 1.24 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: 3.33 Time building geometry restraints manager: 4.41 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: 98.69 - 105.77: 229 105.77 - 112.85: 6171 112.85 - 119.93: 3716 119.93 - 127.00: 5148 127.00 - 134.08: 104 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 2.440 nonbonded pdb=" OG1 THR B 19 " pdb=" OG SER B 139 " model vdw 2.209 2.440 nonbonded pdb=" NZ LYS A 461 " pdb=" OE1 GLU A 524 " model vdw 2.213 2.520 nonbonded pdb=" OH TYR C 305 " pdb=" OD2 ASP D 259 " model vdw 2.218 2.440 nonbonded pdb=" OD1 ASN B 66 " pdb=" OG SER B 69 " model vdw 2.228 2.440 ... (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 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.870 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.980 Find NCS groups from input model: 0.410 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.310 ------------------------------------------------------------------------------- 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 : 1.134 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: 1.3096 time to fit residues: 442.5561 Evaluate side-chains 294 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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: 2.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 0.0010 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN 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: 0.7947 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11381 Z= 0.273 Angle : 0.503 6.657 15368 Z= 0.266 Chirality : 0.042 0.135 1722 Planarity : 0.003 0.043 1977 Dihedral : 4.285 18.720 1489 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.67 % Allowed : 7.53 % Favored : 90.80 % 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: 2.05 (0.27), residues: 394 sheet: 1.07 (0.33), 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 0.006 0.001 HIS D 220 PHE 0.020 0.002 PHE B 409 TYR 0.014 0.001 TYR A 103 ARG 0.005 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 315 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 294 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 516 LYS cc_start: 0.7989 (mptt) cc_final: 0.7767 (mptm) REVERT: B 133 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8316 (mt-10) outliers start: 21 outliers final: 13 residues processed: 297 average time/residue: 1.3275 time to fit residues: 421.6326 Evaluate side-chains 310 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 297 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 256 THR 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 258 ASP 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: 0.6980 chunk 38 optimal weight: 0.2980 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 66 ASN B 119 GLN B 352 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11381 Z= 0.215 Angle : 0.464 6.016 15368 Z= 0.248 Chirality : 0.041 0.135 1722 Planarity : 0.003 0.045 1977 Dihedral : 4.211 17.992 1489 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.14 % Allowed : 9.28 % Favored : 88.58 % 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: 2.09 (0.27), residues: 394 sheet: 1.09 (0.32), residues: 259 loop : -0.70 (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 71 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 326 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 299 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 333 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 133 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8316 (mt-10) REVERT: C 329 MET cc_start: 0.6296 (mmm) cc_final: 0.5830 (mmm) REVERT: D 321 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8424 (mtpp) outliers start: 27 outliers final: 13 residues processed: 303 average time/residue: 1.3109 time to fit residues: 425.7320 Evaluate side-chains 313 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 299 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 434 MET 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 176 ASP Chi-restraints excluded: chain D residue 258 ASP 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 123 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.0030 chunk 35 optimal weight: 1.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 110 ASN A 278 GLN B 22 ASN B 50 ASN B 119 GLN B 352 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1018 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= 0.267 Angle : 0.485 6.638 15368 Z= 0.257 Chirality : 0.042 0.133 1722 Planarity : 0.003 0.035 1977 Dihedral : 4.271 17.771 1489 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.14 % Allowed : 10.55 % Favored : 87.31 % 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: 0.66 (0.23), residues: 1372 helix: 2.02 (0.27), residues: 394 sheet: 1.05 (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 0.005 0.001 HIS B 511 PHE 0.021 0.002 PHE B 409 TYR 0.010 0.001 TYR A 71 ARG 0.004 0.000 ARG A 399 *********************** 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 321 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 294 time to evaluate : 1.397 Fit side-chains REVERT: A 81 ASP cc_start: 0.7333 (m-30) cc_final: 0.7018 (m-30) REVERT: A 333 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7834 (mt-10) REVERT: B 133 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8321 (mt-10) REVERT: C 329 MET cc_start: 0.6363 (mmm) cc_final: 0.5867 (mmm) REVERT: D 321 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8372 (mtpp) outliers start: 27 outliers final: 17 residues processed: 299 average time/residue: 1.2885 time to fit residues: 412.9808 Evaluate side-chains 310 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 292 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 197 ILE 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 302 VAL Chi-restraints excluded: chain D residue 321 LYS 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: 1.9990 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 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 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: 0.7940 moved from start: 0.1080 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= 0.210 Angle : 0.466 6.106 15368 Z= 0.247 Chirality : 0.041 0.139 1722 Planarity : 0.003 0.035 1977 Dihedral : 4.198 17.561 1489 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.14 % Allowed : 11.42 % 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: 0.72 (0.23), residues: 1372 helix: 2.10 (0.27), residues: 394 sheet: 1.12 (0.32), residues: 258 loop : -0.71 (0.24), 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 0.011 0.001 TYR A 103 ARG 0.004 0.000 ARG A 399 *********************** 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 321 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 294 time to evaluate : 0.983 Fit side-chains REVERT: A 333 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 371 GLU cc_start: 0.6901 (tt0) cc_final: 0.6683 (tt0) REVERT: B 457 LEU cc_start: 0.8680 (tp) cc_final: 0.8472 (tp) REVERT: C 329 MET cc_start: 0.6375 (mmm) cc_final: 0.5899 (mmm) REVERT: D 321 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8365 (mtpp) outliers start: 27 outliers final: 20 residues processed: 300 average time/residue: 1.2708 time to fit residues: 408.3320 Evaluate side-chains 323 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 302 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 197 ILE 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 232 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 278 GLN B 22 ASN B 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1139 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= 0.222 Angle : 0.473 6.273 15368 Z= 0.250 Chirality : 0.041 0.143 1722 Planarity : 0.003 0.036 1977 Dihedral : 4.212 17.555 1489 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.38 % Allowed : 11.66 % Favored : 85.96 % 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: 2.09 (0.27), residues: 394 sheet: 1.13 (0.32), residues: 258 loop : -0.72 (0.24), 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 103 ARG 0.004 0.000 ARG A 258 *********************** 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 335 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 305 time to evaluate : 1.309 Fit side-chains REVERT: A 115 ARG cc_start: 0.8568 (mtt180) cc_final: 0.8078 (mtt180) REVERT: A 333 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 329 MET cc_start: 0.6419 (mmm) cc_final: 0.5902 (mmm) REVERT: D 321 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8371 (mtpp) outliers start: 30 outliers final: 22 residues processed: 314 average time/residue: 1.3159 time to fit residues: 441.7850 Evaluate side-chains 315 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 292 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 251 THR 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 441 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 197 ILE 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 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 Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 96 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 81 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 110 ASN A 152 ASN A 278 GLN A 416 GLN B 22 ASN B 43 GLN B 119 GLN B 269 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11381 Z= 0.181 Angle : 0.464 7.442 15368 Z= 0.245 Chirality : 0.041 0.139 1722 Planarity : 0.003 0.047 1977 Dihedral : 4.125 17.465 1489 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.46 % Allowed : 12.05 % Favored : 85.49 % 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: 0.76 (0.23), residues: 1372 helix: 2.17 (0.27), residues: 394 sheet: 1.13 (0.32), residues: 258 loop : -0.70 (0.24), 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 0.017 0.001 PHE B 409 TYR 0.015 0.001 TYR A 103 ARG 0.011 0.000 ARG A 130 *********************** 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 327 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 296 time to evaluate : 1.228 Fit side-chains REVERT: C 329 MET cc_start: 0.6428 (mmm) cc_final: 0.5914 (mmm) REVERT: D 321 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8359 (mtpp) outliers start: 31 outliers final: 22 residues processed: 306 average time/residue: 1.2731 time to fit residues: 418.4140 Evaluate side-chains 320 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 297 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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 251 THR 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 441 ASP Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 527 GLN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 269 GLN B 352 GLN ** B 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11381 Z= 0.419 Angle : 0.563 7.759 15368 Z= 0.293 Chirality : 0.045 0.146 1722 Planarity : 0.004 0.039 1977 Dihedral : 4.486 17.906 1489 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.38 % Allowed : 12.69 % 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: 0.54 (0.23), residues: 1372 helix: 1.87 (0.26), residues: 393 sheet: 0.97 (0.31), residues: 273 loop : -0.79 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 276 HIS 0.007 0.001 HIS B 246 PHE 0.025 0.002 PHE B 409 TYR 0.014 0.002 TYR A 71 ARG 0.007 0.001 ARG C 210 *********************** 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 325 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 295 time to evaluate : 1.323 Fit side-chains REVERT: A 134 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7218 (ttp) REVERT: A 172 GLU cc_start: 0.7064 (tp30) cc_final: 0.6862 (tp30) REVERT: C 329 MET cc_start: 0.6401 (mmm) cc_final: 0.5897 (mmm) REVERT: D 321 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8387 (mtpp) outliers start: 30 outliers final: 24 residues processed: 304 average time/residue: 1.2601 time to fit residues: 411.0301 Evaluate side-chains 321 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 295 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 371 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 441 ASP Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 0.0040 chunk 37 optimal weight: 0.0270 chunk 111 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.4250 ------------------------------------------------------------------------------- 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: 0.7929 moved from start: 0.1318 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= 0.167 Angle : 0.479 7.746 15368 Z= 0.252 Chirality : 0.041 0.153 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.176 17.502 1489 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.22 % Allowed : 13.48 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.11 (0.27), residues: 394 sheet: 1.12 (0.32), residues: 258 loop : -0.71 (0.24), 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 0.016 0.001 TYR A 103 ARG 0.007 0.000 ARG A 130 *********************** 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 318 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 290 time to evaluate : 1.216 Fit side-chains REVERT: A 329 LEU cc_start: 0.8275 (mp) cc_final: 0.8015 (mt) REVERT: B 142 PHE cc_start: 0.8796 (p90) cc_final: 0.8520 (p90) REVERT: C 329 MET cc_start: 0.6397 (mmm) cc_final: 0.5883 (mmm) REVERT: D 321 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8360 (mtpp) outliers start: 28 outliers final: 22 residues processed: 298 average time/residue: 1.3144 time to fit residues: 418.9068 Evaluate side-chains 310 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 287 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 249 LYS Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 371 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 441 ASP Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 64 THR 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 228 ASP 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 Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11381 Z= 0.219 Angle : 0.495 7.665 15368 Z= 0.259 Chirality : 0.041 0.152 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.219 17.503 1489 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.98 % Allowed : 13.72 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.10 (0.26), residues: 394 sheet: 1.06 (0.32), residues: 260 loop : -0.70 (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 0.019 0.001 PHE B 409 TYR 0.015 0.001 TYR A 103 ARG 0.007 0.000 ARG A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 288 time to evaluate : 1.181 Fit side-chains REVERT: C 329 MET cc_start: 0.6405 (mmm) cc_final: 0.5897 (mmm) REVERT: D 321 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8365 (mtpp) outliers start: 25 outliers final: 19 residues processed: 298 average time/residue: 1.3342 time to fit residues: 424.9270 Evaluate side-chains 307 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 287 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 249 LYS Chi-restraints excluded: chain A residue 251 THR 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 441 ASP Chi-restraints excluded: chain B residue 64 THR 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 228 ASP 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 Chi-restraints excluded: chain D residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5639 > 50: distance: 25 - 130: 26.809 distance: 28 - 127: 6.832 distance: 37 - 112: 7.186 distance: 40 - 109: 15.842 distance: 59 - 69: 6.657 distance: 69 - 70: 4.074 distance: 70 - 71: 3.040 distance: 70 - 73: 6.225 distance: 71 - 72: 7.726 distance: 71 - 77: 9.244 distance: 73 - 74: 11.730 distance: 74 - 75: 10.587 distance: 77 - 78: 10.357 distance: 78 - 79: 16.127 distance: 78 - 81: 11.578 distance: 79 - 80: 15.581 distance: 79 - 88: 19.964 distance: 81 - 82: 4.037 distance: 82 - 83: 4.618 distance: 85 - 87: 3.088 distance: 88 - 89: 13.240 distance: 88 - 94: 18.332 distance: 89 - 90: 8.480 distance: 89 - 92: 3.009 distance: 90 - 91: 10.234 distance: 90 - 95: 9.896 distance: 92 - 93: 3.293 distance: 93 - 94: 7.490 distance: 95 - 96: 4.005 distance: 96 - 97: 13.917 distance: 96 - 99: 7.189 distance: 97 - 98: 17.713 distance: 97 - 101: 24.318 distance: 99 - 100: 9.201 distance: 101 - 102: 17.489 distance: 101 - 237: 21.508 distance: 102 - 103: 16.715 distance: 102 - 105: 11.015 distance: 103 - 104: 24.680 distance: 103 - 109: 23.984 distance: 104 - 234: 14.699 distance: 105 - 106: 11.980 distance: 106 - 107: 12.507 distance: 106 - 108: 12.722 distance: 109 - 110: 9.733 distance: 110 - 111: 11.218 distance: 110 - 113: 6.956 distance: 111 - 112: 15.123 distance: 111 - 120: 9.802 distance: 113 - 114: 4.794 distance: 114 - 115: 3.850 distance: 114 - 116: 9.875 distance: 115 - 117: 7.369 distance: 116 - 118: 11.848 distance: 117 - 119: 9.475 distance: 118 - 119: 11.671 distance: 120 - 121: 20.047 distance: 120 - 222: 21.033 distance: 121 - 122: 20.398 distance: 121 - 124: 24.282 distance: 122 - 123: 21.206 distance: 122 - 127: 6.650 distance: 123 - 219: 7.319 distance: 124 - 125: 31.229 distance: 124 - 126: 5.569 distance: 127 - 128: 7.544 distance: 128 - 129: 11.028 distance: 128 - 131: 13.788 distance: 129 - 130: 15.462 distance: 129 - 139: 36.490 distance: 131 - 132: 11.824 distance: 132 - 133: 9.280 distance: 132 - 134: 7.268 distance: 133 - 135: 10.134 distance: 134 - 136: 5.370 distance: 135 - 137: 4.557 distance: 136 - 137: 10.237 distance: 137 - 138: 20.668 distance: 139 - 140: 16.341 distance: 139 - 145: 24.268 distance: 140 - 141: 16.350 distance: 140 - 143: 29.442 distance: 141 - 142: 24.350 distance: 141 - 146: 12.614 distance: 143 - 144: 15.470 distance: 144 - 145: 24.016 distance: 146 - 147: 17.971 distance: 147 - 148: 27.322 distance: 147 - 150: 8.289 distance: 148 - 149: 10.537 distance: 148 - 155: 9.815 distance: 150 - 151: 19.667 distance: 151 - 152: 18.901 distance: 152 - 153: 22.141 distance: 152 - 154: 25.677