Starting phenix.real_space_refine on Sat Dec 9 13:19:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/12_2023/8ag4_15415.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/12_2023/8ag4_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_15415/12_2023/8ag4_15415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/12_2023/8ag4_15415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/12_2023/8ag4_15415.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag4_15415/12_2023/8ag4_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-1.21rc1-5172/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: 6.16, per 1000 atoms: 0.55 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: 4.03 Conformation dependent library (CDL) restraints added in 1.9 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: 1.21 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: 3.22 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.170 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 31.160 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.690 ------------------------------------------------------------------------------- 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 : 1.306 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 1.3273 time to fit residues: 449.1174 Evaluate side-chains 294 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8689 ------------------------------------------------------------------------------- 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: 0.7946 moved from start: 0.0769 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= 0.274 Angle : 0.503 6.611 15368 Z= 0.266 Chirality : 0.042 0.134 1722 Planarity : 0.003 0.043 1977 Dihedral : 4.283 18.753 1489 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.67 % Allowed : 7.77 % Favored : 90.56 % 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 : 1.312 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 297 average time/residue: 1.3201 time to fit residues: 420.1764 Evaluate side-chains 311 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 297 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 3 residues processed: 11 average time/residue: 0.3134 time to fit residues: 6.1939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 352 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11381 Z= 0.251 Angle : 0.481 6.377 15368 Z= 0.256 Chirality : 0.042 0.134 1722 Planarity : 0.003 0.044 1977 Dihedral : 4.281 18.037 1489 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.22 % Allowed : 9.12 % Favored : 88.66 % 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: 0.67 (0.23), residues: 1372 helix: 2.02 (0.27), residues: 394 sheet: 1.09 (0.33), residues: 259 loop : -0.72 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.021 0.001 PHE B 409 TYR 0.011 0.001 TYR A 103 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 328 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 300 time to evaluate : 1.350 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 304 average time/residue: 1.3182 time to fit residues: 429.5439 Evaluate side-chains 318 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 302 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 2 residues processed: 14 average time/residue: 0.3422 time to fit residues: 7.6953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.0040 chunk 35 optimal weight: 1.9990 overall best weight: 1.2176 ------------------------------------------------------------------------------- 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 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7965 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 : 0.005 0.041 11381 Z= 0.355 Angle : 0.523 7.204 15368 Z= 0.275 Chirality : 0.044 0.134 1722 Planarity : 0.003 0.039 1977 Dihedral : 4.417 18.090 1489 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.98 % Allowed : 11.42 % Favored : 86.60 % 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: 0.57 (0.23), residues: 1372 helix: 1.92 (0.26), residues: 393 sheet: 1.08 (0.32), residues: 261 loop : -0.79 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 247 HIS 0.006 0.001 HIS D 220 PHE 0.023 0.002 PHE B 409 TYR 0.013 0.002 TYR A 71 ARG 0.004 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 329 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 304 time to evaluate : 1.363 Fit side-chains outliers start: 25 outliers final: 16 residues processed: 307 average time/residue: 1.2957 time to fit residues: 427.3478 Evaluate side-chains 319 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 303 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 3 residues processed: 13 average time/residue: 0.3056 time to fit residues: 6.7839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 118 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 B 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1164 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= 0.195 Angle : 0.467 6.718 15368 Z= 0.247 Chirality : 0.041 0.142 1722 Planarity : 0.003 0.038 1977 Dihedral : 4.232 17.750 1489 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.14 % Allowed : 11.90 % 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: 0.72 (0.23), residues: 1372 helix: 2.12 (0.27), residues: 394 sheet: 1.16 (0.32), residues: 257 loop : -0.74 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.019 0.001 PHE B 409 TYR 0.009 0.001 TYR A 71 ARG 0.009 0.000 ARG A 130 *********************** 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 327 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 300 time to evaluate : 1.344 Fit side-chains outliers start: 27 outliers final: 19 residues processed: 308 average time/residue: 1.2954 time to fit residues: 428.8474 Evaluate side-chains 319 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 300 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 7 residues processed: 12 average time/residue: 0.3812 time to fit residues: 7.3919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 278 GLN B 22 ASN B 43 GLN B 50 ASN B 119 GLN B 269 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11381 Z= 0.255 Angle : 0.494 7.990 15368 Z= 0.259 Chirality : 0.042 0.144 1722 Planarity : 0.003 0.039 1977 Dihedral : 4.287 17.819 1489 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.22 % Allowed : 12.05 % Favored : 85.73 % 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: 0.68 (0.23), residues: 1372 helix: 2.06 (0.26), residues: 394 sheet: 1.14 (0.32), residues: 258 loop : -0.76 (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 0.021 0.001 PHE B 409 TYR 0.013 0.001 TYR A 103 ARG 0.008 0.000 ARG A 130 *********************** 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 323 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 295 time to evaluate : 1.383 Fit side-chains outliers start: 28 outliers final: 21 residues processed: 304 average time/residue: 1.3377 time to fit residues: 436.4993 Evaluate side-chains 308 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 287 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 9 residues processed: 12 average time/residue: 0.5192 time to fit residues: 9.1775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 0.0670 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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 43 GLN B 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11381 Z= 0.175 Angle : 0.467 7.352 15368 Z= 0.246 Chirality : 0.041 0.158 1722 Planarity : 0.003 0.037 1977 Dihedral : 4.147 17.456 1489 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.82 % Allowed : 13.24 % 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: 0.77 (0.23), residues: 1372 helix: 2.20 (0.27), residues: 394 sheet: 1.06 (0.32), residues: 262 loop : -0.70 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 247 HIS 0.005 0.001 HIS D 220 PHE 0.018 0.001 PHE B 409 TYR 0.009 0.001 TYR A 103 ARG 0.007 0.000 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 309 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 286 time to evaluate : 1.304 Fit side-chains outliers start: 23 outliers final: 20 residues processed: 296 average time/residue: 1.3217 time to fit residues: 419.8901 Evaluate side-chains 304 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 284 time to evaluate : 1.468 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 10 residues processed: 10 average time/residue: 0.6136 time to fit residues: 8.7936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.0470 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 83 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.0030 chunk 103 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.3488 ------------------------------------------------------------------------------- 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 43 GLN B 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1354 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= 0.147 Angle : 0.465 9.814 15368 Z= 0.242 Chirality : 0.040 0.135 1722 Planarity : 0.003 0.036 1977 Dihedral : 4.068 19.820 1489 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.35 % Allowed : 13.80 % 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: 0.81 (0.23), residues: 1372 helix: 2.27 (0.27), residues: 394 sheet: 1.06 (0.32), residues: 261 loop : -0.67 (0.24), residues: 717 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 0.021 0.001 TYR A 103 ARG 0.009 0.000 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 310 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 293 time to evaluate : 1.369 Fit side-chains outliers start: 17 outliers final: 15 residues processed: 304 average time/residue: 1.3082 time to fit residues: 427.5875 Evaluate side-chains 306 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 291 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.7414 time to fit residues: 6.1300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 1.9990 chunk 123 optimal weight: 0.0060 chunk 126 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 0.0020 chunk 37 optimal weight: 0.2980 chunk 111 optimal weight: 0.0870 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.2182 ------------------------------------------------------------------------------- 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 101 ASN A 106 GLN A 110 ASN A 278 GLN A 416 GLN ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 43 GLN B 119 GLN B 352 GLN D 328 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11381 Z= 0.125 Angle : 0.462 9.003 15368 Z= 0.239 Chirality : 0.040 0.132 1722 Planarity : 0.003 0.033 1977 Dihedral : 3.927 17.317 1489 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.74 % Allowed : 14.12 % Favored : 84.14 % 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: 0.91 (0.24), residues: 1372 helix: 2.35 (0.27), residues: 394 sheet: 1.16 (0.33), residues: 254 loop : -0.62 (0.24), residues: 724 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 0.014 0.001 PHE B 409 TYR 0.011 0.001 TYR A 103 ARG 0.007 0.000 ARG C 210 *********************** 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 313 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 1.220 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 303 average time/residue: 1.2986 time to fit residues: 423.6230 Evaluate side-chains 296 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 284 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 1.0844 time to fit residues: 5.5389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 125 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 66 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 119 GLN B 200 GLN B 352 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11381 Z= 0.160 Angle : 0.475 8.496 15368 Z= 0.245 Chirality : 0.040 0.132 1722 Planarity : 0.003 0.033 1977 Dihedral : 3.949 17.385 1489 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.35 % Allowed : 14.59 % Favored : 84.06 % 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: 0.91 (0.24), residues: 1372 helix: 2.37 (0.27), residues: 394 sheet: 1.04 (0.32), residues: 261 loop : -0.59 (0.24), residues: 717 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 0.016 0.001 PHE B 409 TYR 0.015 0.001 TYR A 103 ARG 0.008 0.000 ARG C 210 ********************** 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 303 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 286 time to evaluate : 1.242 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 296 average time/residue: 1.3031 time to fit residues: 414.3876 Evaluate side-chains 293 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 282 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.4166 time to fit residues: 3.3196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 100 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 119 GLN B 200 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 = 0.3918 r_free = 0.3918 target = 0.147743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118788 restraints weight = 13991.232| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.99 r_work: 0.3408 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1449 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= 0.182 Angle : 0.486 8.278 15368 Z= 0.252 Chirality : 0.041 0.133 1722 Planarity : 0.003 0.033 1977 Dihedral : 3.999 17.385 1489 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.87 % Allowed : 15.07 % Favored : 84.06 % 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: 0.91 (0.23), residues: 1372 helix: 2.35 (0.27), residues: 394 sheet: 1.11 (0.32), residues: 257 loop : -0.60 (0.24), residues: 721 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 0.017 0.001 PHE B 409 TYR 0.025 0.001 TYR A 103 ARG 0.009 0.000 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6478.08 seconds wall clock time: 114 minutes 20.45 seconds (6860.45 seconds total)