Starting phenix.real_space_refine on Sat Aug 3 20:23:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/08_2024/8tsp_41597.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/08_2024/8tsp_41597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/08_2024/8tsp_41597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/08_2024/8tsp_41597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/08_2024/8tsp_41597.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/08_2024/8tsp_41597.cif" } resolution = 3.9 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= 0.043 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 54 5.16 5 C 5630 2.51 5 N 1548 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8888 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4444 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 13, 'TRANS': 559} Chain: "B" Number of atoms: 4444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4444 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 13, 'TRANS': 559} Time building chain proxies: 5.09, per 1000 atoms: 0.57 Number of scatterers: 8888 At special positions: 0 Unit cell: (67.095, 122.475, 136.32, 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 54 16.00 O 1656 8.00 N 1548 7.00 C 5630 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: 3.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 6 sheets defined 69.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 10 through 21 removed outlier: 4.044A pdb=" N ARG A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A) Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 23 through 47 removed outlier: 3.678A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.685A pdb=" N LEU A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 109 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 112 through 119 removed outlier: 4.286A pdb=" N PHE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 163 removed outlier: 3.899A pdb=" N LEU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 133 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 148 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 213 removed outlier: 3.774A pdb=" N SER A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 224 through 272 Proline residue: A 253 - end of helix removed outlier: 3.681A pdb=" N PHE A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.594A pdb=" N ILE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 323 removed outlier: 3.526A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.634A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 471 Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 512 through 526 Processing helix chain 'A' and resid 538 through 544 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'B' and resid 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 10 through 21 removed outlier: 4.048A pdb=" N ARG B 14 " --> pdb=" O TRP B 10 " (cutoff:3.500A) Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 23 through 47 removed outlier: 3.674A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.702A pdb=" N LEU B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 109 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 112 through 119 removed outlier: 4.153A pdb=" N PHE B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 163 removed outlier: 3.587A pdb=" N LEU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 133 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 213 removed outlier: 3.632A pdb=" N SER B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 224 through 272 Proline residue: B 253 - end of helix removed outlier: 3.661A pdb=" N PHE B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 4.012A pdb=" N THR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 323 removed outlier: 3.538A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 468 through 471 Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 512 through 526 Processing helix chain 'B' and resid 538 through 544 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 570 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366 removed outlier: 6.390A pdb=" N ARG A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THR A 348 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE A 362 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN A 346 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 342 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE A 344 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A 401 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASN A 346 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU A 399 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422 removed outlier: 3.788A pdb=" N ILE A 503 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 422 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 535 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 504 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A 558 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N GLU A 552 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 366 removed outlier: 5.082A pdb=" N ARG B 360 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE B 349 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU B 364 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG B 345 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE B 366 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU B 343 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL B 347 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLU B 397 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET B 402 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS B 405 " --> pdb=" O MET B 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 419 through 422 removed outlier: 6.726A pdb=" N ALA B 420 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASP B 505 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 422 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 372 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 547 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B 558 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU B 552 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 431 through 432 581 hydrogen bonds defined for protein. 1722 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: 2.61 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2781 1.34 - 1.46: 1587 1.46 - 1.58: 4546 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 9018 Sorted by residual: bond pdb=" N VAL B 555 " pdb=" CA VAL B 555 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N ILE B 250 " pdb=" CA ILE B 250 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.09e-02 8.42e+03 9.88e+00 bond pdb=" N ASP B 252 " pdb=" CA ASP B 252 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.67e+00 bond pdb=" N VAL A 551 " pdb=" CA VAL A 551 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.67e+00 bond pdb=" N ILE B 177 " pdb=" CA ILE B 177 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.42e+00 ... (remaining 9013 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.16: 133 105.16 - 112.36: 4714 112.36 - 119.56: 3020 119.56 - 126.77: 4249 126.77 - 133.97: 72 Bond angle restraints: 12188 Sorted by residual: angle pdb=" N ILE B 250 " pdb=" CA ILE B 250 " pdb=" C ILE B 250 " ideal model delta sigma weight residual 113.43 108.13 5.30 1.09e+00 8.42e-01 2.37e+01 angle pdb=" CB MET A 295 " pdb=" CG MET A 295 " pdb=" SD MET A 295 " ideal model delta sigma weight residual 112.70 125.67 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" N ASN A 477 " pdb=" CA ASN A 477 " pdb=" C ASN A 477 " ideal model delta sigma weight residual 111.81 106.25 5.56 1.54e+00 4.22e-01 1.30e+01 angle pdb=" CA ASP A 553 " pdb=" C ASP A 553 " pdb=" O ASP A 553 " ideal model delta sigma weight residual 121.84 117.67 4.17 1.16e+00 7.43e-01 1.29e+01 angle pdb=" N ASN B 477 " pdb=" CA ASN B 477 " pdb=" C ASN B 477 " ideal model delta sigma weight residual 111.81 106.32 5.49 1.54e+00 4.22e-01 1.27e+01 ... (remaining 12183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4718 17.83 - 35.65: 594 35.65 - 53.48: 143 53.48 - 71.31: 29 71.31 - 89.14: 8 Dihedral angle restraints: 5492 sinusoidal: 2178 harmonic: 3314 Sorted by residual: dihedral pdb=" CA ARG B 391 " pdb=" C ARG B 391 " pdb=" N PHE B 392 " pdb=" CA PHE B 392 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER A 249 " pdb=" C SER A 249 " pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP A 471 " pdb=" CB ASP A 471 " pdb=" CG ASP A 471 " pdb=" OD1 ASP A 471 " ideal model delta sinusoidal sigma weight residual -30.00 -87.41 57.41 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1016 0.042 - 0.085: 313 0.085 - 0.127: 86 0.127 - 0.170: 27 0.170 - 0.212: 10 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CA ILE A 556 " pdb=" N ILE A 556 " pdb=" C ILE A 556 " pdb=" CB ILE A 556 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE B 255 " pdb=" N ILE B 255 " pdb=" C ILE B 255 " pdb=" CB ILE B 255 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA ILE B 180 " pdb=" N ILE B 180 " pdb=" C ILE B 180 " pdb=" CB ILE B 180 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 1449 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 186 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C SER A 186 " 0.036 2.00e-02 2.50e+03 pdb=" O SER A 186 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 187 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 184 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C VAL A 184 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL A 184 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 185 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 184 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C VAL B 184 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL B 184 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL B 185 " -0.012 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 788 2.74 - 3.28: 9452 3.28 - 3.82: 14911 3.82 - 4.36: 16760 4.36 - 4.90: 28594 Nonbonded interactions: 70505 Sorted by model distance: nonbonded pdb=" O THR B 9 " pdb=" OG1 THR B 12 " model vdw 2.201 3.040 nonbonded pdb=" O THR A 9 " pdb=" OG1 THR A 12 " model vdw 2.205 3.040 nonbonded pdb=" ND2 ASN A 430 " pdb=" OE1 GLN B 209 " model vdw 2.261 3.120 nonbonded pdb=" NH1 ARG A 102 " pdb=" OD1 ASP B 231 " model vdw 2.283 3.120 nonbonded pdb=" O GLU A 224 " pdb=" OG1 THR A 227 " model vdw 2.299 3.040 ... (remaining 70500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.120 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 0.004 0.038 9018 Z= 0.278 Angle : 0.752 12.969 12188 Z= 0.470 Chirality : 0.048 0.212 1452 Planarity : 0.005 0.066 1542 Dihedral : 16.525 89.137 3348 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.72 % Allowed : 23.26 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.25), residues: 1142 helix: 1.08 (0.20), residues: 714 sheet: 0.37 (0.61), residues: 78 loop : -1.15 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 66 HIS 0.008 0.001 HIS A 214 PHE 0.019 0.002 PHE A 115 TYR 0.015 0.001 TYR A 445 ARG 0.011 0.001 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 295 MET cc_start: 0.5770 (mmm) cc_final: 0.5148 (mtt) REVERT: B 111 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.5796 (mpp) REVERT: B 117 ASP cc_start: 0.5455 (m-30) cc_final: 0.5115 (m-30) REVERT: B 283 THR cc_start: 0.8056 (p) cc_final: 0.7597 (t) REVERT: B 312 MET cc_start: 0.8902 (mmt) cc_final: 0.8416 (mmt) REVERT: B 363 ASN cc_start: 0.5549 (m-40) cc_final: 0.5337 (t0) outliers start: 7 outliers final: 3 residues processed: 155 average time/residue: 0.2381 time to fit residues: 49.3052 Evaluate side-chains 136 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 356 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN B 107 HIS B 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9018 Z= 0.277 Angle : 0.627 7.546 12188 Z= 0.331 Chirality : 0.043 0.158 1452 Planarity : 0.004 0.037 1542 Dihedral : 4.515 44.255 1253 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.41 % Allowed : 22.44 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.25), residues: 1142 helix: 1.54 (0.19), residues: 728 sheet: 0.41 (0.57), residues: 78 loop : -0.96 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 66 HIS 0.005 0.001 HIS B 107 PHE 0.025 0.002 PHE B 56 TYR 0.010 0.002 TYR A 87 ARG 0.005 0.001 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7691 (tpp) cc_final: 0.7433 (ttm) REVERT: A 291 MET cc_start: 0.7913 (mmm) cc_final: 0.7590 (tmm) REVERT: A 330 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7777 (pm20) REVERT: B 301 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7456 (mp) outliers start: 43 outliers final: 22 residues processed: 176 average time/residue: 0.2086 time to fit residues: 50.6537 Evaluate side-chains 159 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 526 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9018 Z= 0.374 Angle : 0.701 8.789 12188 Z= 0.365 Chirality : 0.046 0.142 1452 Planarity : 0.004 0.036 1542 Dihedral : 4.457 23.759 1248 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 7.17 % Allowed : 22.85 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.25), residues: 1142 helix: 1.53 (0.20), residues: 716 sheet: 0.27 (0.55), residues: 78 loop : -0.88 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 66 HIS 0.007 0.001 HIS A 214 PHE 0.020 0.003 PHE A 56 TYR 0.012 0.002 TYR B 83 ARG 0.005 0.001 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 132 time to evaluate : 0.986 Fit side-chains REVERT: A 44 MET cc_start: 0.7981 (tpp) cc_final: 0.7522 (ttm) REVERT: A 330 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7845 (pm20) REVERT: A 341 ASP cc_start: 0.6064 (OUTLIER) cc_final: 0.5672 (m-30) REVERT: B 167 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8435 (tt) REVERT: B 200 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.5179 (tpt) REVERT: B 301 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7605 (mp) outliers start: 70 outliers final: 48 residues processed: 190 average time/residue: 0.1995 time to fit residues: 52.5520 Evaluate side-chains 177 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 124 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 0.1980 chunk 110 optimal weight: 0.0970 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9018 Z= 0.178 Angle : 0.536 4.963 12188 Z= 0.286 Chirality : 0.041 0.149 1452 Planarity : 0.003 0.034 1542 Dihedral : 4.112 22.810 1248 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.61 % Allowed : 26.02 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.26), residues: 1142 helix: 1.97 (0.20), residues: 718 sheet: 0.33 (0.55), residues: 78 loop : -0.74 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 66 HIS 0.003 0.001 HIS A 214 PHE 0.018 0.002 PHE A 56 TYR 0.010 0.001 TYR A 162 ARG 0.003 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 138 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7889 (tpp) cc_final: 0.7422 (ttm) REVERT: A 341 ASP cc_start: 0.5915 (OUTLIER) cc_final: 0.5670 (m-30) REVERT: B 200 MET cc_start: 0.5671 (OUTLIER) cc_final: 0.5125 (tpt) outliers start: 45 outliers final: 27 residues processed: 173 average time/residue: 0.2375 time to fit residues: 55.9192 Evaluate side-chains 152 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 520 GLN B 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9018 Z= 0.282 Angle : 0.608 6.509 12188 Z= 0.319 Chirality : 0.043 0.181 1452 Planarity : 0.004 0.035 1542 Dihedral : 4.225 23.377 1248 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.25 % Allowed : 24.39 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.26), residues: 1142 helix: 1.77 (0.20), residues: 730 sheet: 0.11 (0.55), residues: 80 loop : -0.71 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 66 HIS 0.003 0.001 HIS B 214 PHE 0.016 0.002 PHE A 56 TYR 0.009 0.001 TYR B 83 ARG 0.005 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 124 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8144 (tpp) cc_final: 0.7567 (ttm) REVERT: A 231 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7168 (t70) REVERT: A 341 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5827 (m-30) REVERT: A 402 MET cc_start: 0.7766 (ptp) cc_final: 0.7252 (mtt) REVERT: A 466 MET cc_start: 0.3327 (mmm) cc_final: 0.3070 (mmm) REVERT: B 200 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5201 (tpt) REVERT: B 301 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7576 (mp) REVERT: B 466 MET cc_start: 0.2804 (mmm) cc_final: 0.2591 (mmm) outliers start: 61 outliers final: 45 residues processed: 171 average time/residue: 0.2069 time to fit residues: 48.6726 Evaluate side-chains 166 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 117 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS A 436 ASN B 326 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9018 Z= 0.204 Angle : 0.556 6.074 12188 Z= 0.291 Chirality : 0.042 0.227 1452 Planarity : 0.004 0.034 1542 Dihedral : 4.136 22.927 1248 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.94 % Allowed : 25.20 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.26), residues: 1142 helix: 1.88 (0.20), residues: 730 sheet: 0.10 (0.56), residues: 80 loop : -0.67 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 66 HIS 0.008 0.001 HIS A 405 PHE 0.018 0.002 PHE B 189 TYR 0.007 0.001 TYR A 130 ARG 0.005 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 124 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8146 (tpp) cc_final: 0.7490 (tmm) REVERT: A 341 ASP cc_start: 0.6059 (OUTLIER) cc_final: 0.5765 (m-30) REVERT: A 402 MET cc_start: 0.7652 (ptp) cc_final: 0.7311 (mtt) REVERT: A 456 MET cc_start: 0.8355 (tpp) cc_final: 0.8083 (tpp) REVERT: B 200 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.5315 (tpt) REVERT: B 301 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7262 (mp) outliers start: 58 outliers final: 43 residues processed: 169 average time/residue: 0.2078 time to fit residues: 48.6215 Evaluate side-chains 162 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 116 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.0670 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN B 326 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9018 Z= 0.185 Angle : 0.565 11.076 12188 Z= 0.291 Chirality : 0.041 0.164 1452 Planarity : 0.003 0.033 1542 Dihedral : 4.103 22.800 1248 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.74 % Allowed : 25.31 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.26), residues: 1142 helix: 1.99 (0.19), residues: 730 sheet: 0.15 (0.56), residues: 80 loop : -0.64 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 66 HIS 0.002 0.000 HIS B 107 PHE 0.018 0.001 PHE B 189 TYR 0.007 0.001 TYR B 445 ARG 0.005 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 119 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8159 (tpp) cc_final: 0.7604 (tmm) REVERT: A 341 ASP cc_start: 0.6010 (OUTLIER) cc_final: 0.5754 (m-30) REVERT: A 402 MET cc_start: 0.7603 (ptp) cc_final: 0.7272 (mtt) REVERT: A 456 MET cc_start: 0.8383 (tpp) cc_final: 0.8098 (tpp) REVERT: B 67 MET cc_start: 0.8386 (tpp) cc_final: 0.8137 (mmm) REVERT: B 200 MET cc_start: 0.5896 (tpt) cc_final: 0.5488 (tpt) REVERT: B 301 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7148 (mp) outliers start: 56 outliers final: 45 residues processed: 164 average time/residue: 0.2040 time to fit residues: 46.5322 Evaluate side-chains 162 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 115 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 436 ASN A 537 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9018 Z= 0.190 Angle : 0.571 10.698 12188 Z= 0.292 Chirality : 0.041 0.173 1452 Planarity : 0.004 0.033 1542 Dihedral : 4.108 22.949 1248 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.74 % Allowed : 25.10 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.26), residues: 1142 helix: 1.94 (0.19), residues: 734 sheet: 0.23 (0.61), residues: 70 loop : -0.64 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 66 HIS 0.008 0.001 HIS A 405 PHE 0.018 0.001 PHE B 189 TYR 0.007 0.001 TYR A 130 ARG 0.005 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 120 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8140 (tpp) cc_final: 0.7613 (tmm) REVERT: A 402 MET cc_start: 0.7621 (ptp) cc_final: 0.7329 (mtt) REVERT: A 456 MET cc_start: 0.8376 (tpp) cc_final: 0.8109 (tpp) REVERT: B 67 MET cc_start: 0.8400 (tpp) cc_final: 0.8165 (mmm) REVERT: B 200 MET cc_start: 0.5886 (tpt) cc_final: 0.5486 (tpt) REVERT: B 301 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7070 (mp) outliers start: 56 outliers final: 46 residues processed: 167 average time/residue: 0.2009 time to fit residues: 46.6121 Evaluate side-chains 166 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 119 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 537 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9018 Z= 0.192 Angle : 0.583 11.343 12188 Z= 0.296 Chirality : 0.041 0.169 1452 Planarity : 0.004 0.036 1542 Dihedral : 4.112 23.359 1248 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.33 % Allowed : 25.51 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.26), residues: 1142 helix: 1.98 (0.19), residues: 734 sheet: 0.23 (0.62), residues: 70 loop : -0.57 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 66 HIS 0.008 0.001 HIS A 405 PHE 0.020 0.002 PHE B 189 TYR 0.010 0.001 TYR B 130 ARG 0.006 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 121 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8076 (tpp) cc_final: 0.7601 (tmm) REVERT: A 402 MET cc_start: 0.7575 (ptp) cc_final: 0.7311 (mtt) REVERT: A 456 MET cc_start: 0.8372 (tpp) cc_final: 0.8105 (tpp) REVERT: B 67 MET cc_start: 0.8439 (tpp) cc_final: 0.8171 (mmm) REVERT: B 200 MET cc_start: 0.5890 (tpt) cc_final: 0.5482 (tpt) REVERT: B 301 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7103 (mp) outliers start: 52 outliers final: 49 residues processed: 164 average time/residue: 0.2066 time to fit residues: 47.0741 Evaluate side-chains 165 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 115 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 537 HIS B 405 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9018 Z= 0.207 Angle : 0.597 10.596 12188 Z= 0.303 Chirality : 0.042 0.168 1452 Planarity : 0.004 0.052 1542 Dihedral : 4.152 23.511 1248 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.23 % Allowed : 25.82 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.26), residues: 1142 helix: 1.87 (0.19), residues: 738 sheet: 0.20 (0.63), residues: 70 loop : -0.51 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 66 HIS 0.006 0.001 HIS A 405 PHE 0.020 0.002 PHE B 189 TYR 0.011 0.001 TYR B 445 ARG 0.006 0.000 ARG B 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 117 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8084 (tpp) cc_final: 0.7610 (tmm) REVERT: A 402 MET cc_start: 0.7526 (ptp) cc_final: 0.7296 (mtt) REVERT: A 456 MET cc_start: 0.8370 (tpp) cc_final: 0.8115 (tpp) REVERT: B 67 MET cc_start: 0.8518 (tpp) cc_final: 0.8246 (mmm) REVERT: B 200 MET cc_start: 0.5885 (tpt) cc_final: 0.5454 (tpt) REVERT: B 301 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7060 (mp) outliers start: 51 outliers final: 47 residues processed: 162 average time/residue: 0.2007 time to fit residues: 45.8272 Evaluate side-chains 162 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 0.0020 chunk 16 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 537 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.195334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.182225 restraints weight = 10034.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.179660 restraints weight = 16066.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.178924 restraints weight = 17015.528| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9018 Z= 0.182 Angle : 0.583 10.859 12188 Z= 0.296 Chirality : 0.041 0.168 1452 Planarity : 0.004 0.044 1542 Dihedral : 4.104 23.397 1248 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.33 % Allowed : 25.82 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.70 (0.26), residues: 1142 helix: 1.95 (0.19), residues: 738 sheet: 0.17 (0.63), residues: 70 loop : -0.49 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 66 HIS 0.006 0.001 HIS A 405 PHE 0.020 0.001 PHE B 189 TYR 0.013 0.001 TYR B 445 ARG 0.006 0.000 ARG B 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1811.27 seconds wall clock time: 33 minutes 7.31 seconds (1987.31 seconds total)