Starting phenix.real_space_refine on Fri Jul 19 20:12:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/07_2024/8tsp_41597.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/07_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_41597/07_2024/8tsp_41597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/07_2024/8tsp_41597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/07_2024/8tsp_41597.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tsp_41597/07_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-5388/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: 4.83, per 1000 atoms: 0.54 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: 3.03 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: 0.93 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: 2.88 Time building geometry restraints manager: 3.35 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 2.440 nonbonded pdb=" O THR A 9 " pdb=" OG1 THR A 12 " model vdw 2.205 2.440 nonbonded pdb=" ND2 ASN A 430 " pdb=" OE1 GLN B 209 " model vdw 2.261 2.520 nonbonded pdb=" NH1 ARG A 102 " pdb=" OD1 ASP B 231 " model vdw 2.283 2.520 nonbonded pdb=" O GLU A 224 " pdb=" OG1 THR A 227 " model vdw 2.299 2.440 ... (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 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: 0.850 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.030 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- 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 : 0.962 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: 0.2316 time to fit residues: 47.9749 Evaluate side-chains 136 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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: 8.9990 chunk 86 optimal weight: 0.4980 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS B 316 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9018 Z= 0.272 Angle : 0.613 7.562 12188 Z= 0.322 Chirality : 0.043 0.154 1452 Planarity : 0.004 0.037 1542 Dihedral : 4.532 44.751 1253 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.61 % Allowed : 22.95 % Favored : 72.44 % 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: 1.56 (0.19), residues: 728 sheet: 0.35 (0.56), residues: 78 loop : -1.04 (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 0.024 0.002 PHE B 56 TYR 0.010 0.002 TYR B 83 ARG 0.006 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 186 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 0.979 Fit side-chains REVERT: A 44 MET cc_start: 0.7696 (tpp) cc_final: 0.7424 (ttm) REVERT: A 330 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7754 (pm20) REVERT: B 291 MET cc_start: 0.8186 (mmm) cc_final: 0.7861 (tmm) REVERT: B 301 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7504 (mp) outliers start: 45 outliers final: 27 residues processed: 177 average time/residue: 0.2043 time to fit residues: 49.6868 Evaluate side-chains 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 A residue 531 THR 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 119 GLN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 277 ASP 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 432 THR 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: 5.9990 chunk 86 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9018 Z= 0.213 Angle : 0.549 6.702 12188 Z= 0.290 Chirality : 0.041 0.147 1452 Planarity : 0.004 0.036 1542 Dihedral : 4.079 19.258 1248 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.94 % Allowed : 24.39 % Favored : 69.67 % 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: 1.55 (0.26), residues: 1142 helix: 2.00 (0.20), residues: 718 sheet: 0.49 (0.55), residues: 78 loop : -0.93 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 66 HIS 0.003 0.001 HIS A 107 PHE 0.015 0.002 PHE B 56 TYR 0.008 0.001 TYR B 410 ARG 0.008 0.000 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 199 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 141 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7949 (tpp) cc_final: 0.7461 (ttm) REVERT: A 341 ASP cc_start: 0.5602 (OUTLIER) cc_final: 0.5249 (m-30) REVERT: B 200 MET cc_start: 0.5799 (OUTLIER) cc_final: 0.5132 (tpt) REVERT: B 301 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7417 (mp) REVERT: B 559 ARG cc_start: 0.6882 (mtt90) cc_final: 0.6657 (mtt90) outliers start: 58 outliers final: 36 residues processed: 185 average time/residue: 0.2015 time to fit residues: 51.4835 Evaluate side-chains 167 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 164 SER Chi-restraints excluded: chain A residue 277 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 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 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 89 ILE 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 277 ASP 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 407 LEU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.0030 chunk 77 optimal weight: 0.0980 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 54 optimal weight: 0.0870 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9018 Z= 0.140 Angle : 0.495 5.466 12188 Z= 0.263 Chirality : 0.039 0.152 1452 Planarity : 0.003 0.032 1542 Dihedral : 3.863 19.500 1248 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.48 % Allowed : 26.84 % Favored : 69.67 % 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: 2.00 (0.26), residues: 1142 helix: 2.36 (0.20), residues: 720 sheet: 0.65 (0.58), residues: 66 loop : -0.76 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 66 HIS 0.002 0.001 HIS A 107 PHE 0.017 0.001 PHE B 189 TYR 0.009 0.001 TYR A 162 ARG 0.005 0.000 ARG B 559 *********************** 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 184 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 150 time to evaluate : 0.908 Fit side-chains REVERT: A 44 MET cc_start: 0.7987 (tpp) cc_final: 0.7433 (ttm) REVERT: A 56 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: A 341 ASP cc_start: 0.5042 (OUTLIER) cc_final: 0.4771 (m-30) REVERT: B 200 MET cc_start: 0.5561 (tpt) cc_final: 0.5190 (tpt) REVERT: B 260 SER cc_start: 0.8771 (m) cc_final: 0.8449 (m) outliers start: 34 outliers final: 20 residues processed: 171 average time/residue: 0.2088 time to fit residues: 49.0236 Evaluate side-chains 162 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 56 PHE 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 231 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 317 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 B residue 64 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 284 ILE 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 371 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: 8.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.0170 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9018 Z= 0.379 Angle : 0.684 10.007 12188 Z= 0.354 Chirality : 0.045 0.135 1452 Planarity : 0.004 0.034 1542 Dihedral : 4.381 21.658 1248 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.66 % Allowed : 25.51 % Favored : 67.83 % 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: 1.43 (0.26), residues: 1142 helix: 1.79 (0.20), residues: 726 sheet: 0.63 (0.60), residues: 66 loop : -0.78 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 66 HIS 0.008 0.001 HIS B 405 PHE 0.017 0.003 PHE B 116 TYR 0.013 0.002 TYR B 83 ARG 0.007 0.001 ARG A 333 *********************** 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 194 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 129 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8091 (tpp) cc_final: 0.7599 (ttm) REVERT: A 56 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: A 301 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7797 (mp) REVERT: A 341 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5825 (m-30) REVERT: A 410 TYR cc_start: 0.7155 (m-80) cc_final: 0.6788 (m-10) REVERT: B 34 LEU cc_start: 0.8655 (mt) cc_final: 0.8296 (mt) REVERT: B 301 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7640 (mp) REVERT: B 499 SER cc_start: 0.9175 (OUTLIER) cc_final: 0.8841 (p) outliers start: 65 outliers final: 44 residues processed: 184 average time/residue: 0.2300 time to fit residues: 56.9004 Evaluate side-chains 173 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 124 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 56 PHE 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 164 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 301 LEU 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 432 THR Chi-restraints excluded: chain A residue 531 THR 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 69 LEU Chi-restraints excluded: chain B residue 89 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 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 499 SER Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 0.0010 chunk 110 optimal weight: 0.0670 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.7526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 HIS B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9018 Z= 0.188 Angle : 0.546 13.406 12188 Z= 0.282 Chirality : 0.041 0.143 1452 Planarity : 0.003 0.032 1542 Dihedral : 4.045 20.393 1248 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.10 % Allowed : 29.00 % Favored : 66.91 % 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: 1.76 (0.26), residues: 1142 helix: 2.08 (0.20), residues: 730 sheet: 0.56 (0.57), residues: 78 loop : -0.74 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 66 HIS 0.008 0.001 HIS B 405 PHE 0.018 0.002 PHE B 189 TYR 0.014 0.001 TYR B 445 ARG 0.005 0.000 ARG A 488 *********************** 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 169 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8032 (tpp) cc_final: 0.7484 (tmm) REVERT: A 56 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: A 67 MET cc_start: 0.8102 (tpp) cc_final: 0.7865 (mpp) REVERT: A 301 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7574 (mp) REVERT: A 341 ASP cc_start: 0.5861 (OUTLIER) cc_final: 0.5612 (m-30) REVERT: A 402 MET cc_start: 0.7517 (ptp) cc_final: 0.7180 (mtt) REVERT: B 200 MET cc_start: 0.5834 (tpt) cc_final: 0.5373 (tpt) outliers start: 40 outliers final: 26 residues processed: 163 average time/residue: 0.2214 time to fit residues: 49.2676 Evaluate side-chains 155 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 301 LEU 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 432 THR 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 54 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 231 ASP 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 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 GLN A 537 HIS B 436 ASN B 537 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9018 Z= 0.194 Angle : 0.557 10.522 12188 Z= 0.285 Chirality : 0.040 0.142 1452 Planarity : 0.003 0.033 1542 Dihedral : 4.061 19.811 1248 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.74 % Allowed : 26.74 % Favored : 67.52 % 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: 1.84 (0.26), residues: 1142 helix: 2.13 (0.20), residues: 732 sheet: 0.58 (0.58), residues: 78 loop : -0.70 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 66 HIS 0.008 0.001 HIS A 405 PHE 0.017 0.002 PHE B 189 TYR 0.011 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 182 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 126 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7993 (tpp) cc_final: 0.7532 (tmm) REVERT: A 56 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7970 (m-10) REVERT: A 67 MET cc_start: 0.8030 (tpp) cc_final: 0.7752 (mpp) REVERT: A 301 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7535 (mp) REVERT: A 341 ASP cc_start: 0.5860 (OUTLIER) cc_final: 0.5624 (m-30) REVERT: A 402 MET cc_start: 0.7424 (ptp) cc_final: 0.7150 (mtt) REVERT: A 466 MET cc_start: 0.3225 (mmm) cc_final: 0.2921 (mmm) REVERT: B 200 MET cc_start: 0.5904 (tpt) cc_final: 0.5490 (tpt) REVERT: B 301 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7176 (mp) outliers start: 56 outliers final: 44 residues processed: 169 average time/residue: 0.2055 time to fit residues: 48.1168 Evaluate side-chains 169 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 121 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 56 PHE Chi-restraints excluded: chain A residue 66 TRP 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 277 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 301 LEU 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 407 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 467 ASP 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 66 TRP Chi-restraints excluded: chain B residue 69 LEU 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 204 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 285 THR 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 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 SER 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: 0.3980 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN B 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3227 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= 0.166 Angle : 0.548 11.835 12188 Z= 0.278 Chirality : 0.040 0.143 1452 Planarity : 0.003 0.032 1542 Dihedral : 3.999 19.816 1248 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.71 % Allowed : 27.25 % Favored : 68.03 % 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: 1.99 (0.26), residues: 1142 helix: 2.20 (0.19), residues: 736 sheet: 0.94 (0.63), residues: 66 loop : -0.58 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 66 HIS 0.010 0.001 HIS A 405 PHE 0.018 0.001 PHE B 189 TYR 0.011 0.001 TYR B 162 ARG 0.004 0.000 ARG A 517 *********************** 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 177 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 131 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8021 (tpp) cc_final: 0.7513 (tmm) REVERT: A 56 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7832 (m-10) REVERT: A 67 MET cc_start: 0.8031 (tpp) cc_final: 0.7767 (mpp) REVERT: A 301 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7368 (mp) REVERT: A 341 ASP cc_start: 0.5763 (OUTLIER) cc_final: 0.5225 (m-30) REVERT: B 200 MET cc_start: 0.5872 (tpt) cc_final: 0.5556 (tpt) REVERT: B 283 THR cc_start: 0.8443 (p) cc_final: 0.8004 (t) REVERT: B 301 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7138 (mp) REVERT: B 436 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7262 (m-40) outliers start: 46 outliers final: 33 residues processed: 167 average time/residue: 0.1906 time to fit residues: 44.7393 Evaluate side-chains 164 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 56 PHE 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 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 317 THR 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 414 SER 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 54 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 66 TRP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 231 ASP 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 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 SER 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: 10.0000 chunk 102 optimal weight: 0.0070 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9018 Z= 0.165 Angle : 0.554 10.313 12188 Z= 0.279 Chirality : 0.040 0.155 1452 Planarity : 0.003 0.032 1542 Dihedral : 3.988 19.670 1248 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.00 % Allowed : 28.18 % Favored : 67.83 % 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: 2.06 (0.26), residues: 1142 helix: 2.26 (0.19), residues: 736 sheet: 0.95 (0.64), residues: 66 loop : -0.57 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 66 HIS 0.009 0.001 HIS B 405 PHE 0.019 0.001 PHE B 189 TYR 0.018 0.001 TYR A 162 ARG 0.004 0.000 ARG B 517 *********************** 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 172 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8118 (tpp) cc_final: 0.7638 (tmm) REVERT: A 56 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7803 (m-10) REVERT: A 301 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7292 (mp) REVERT: A 341 ASP cc_start: 0.5680 (OUTLIER) cc_final: 0.5211 (m-30) REVERT: B 200 MET cc_start: 0.5885 (tpt) cc_final: 0.5542 (tpt) REVERT: B 283 THR cc_start: 0.8348 (p) cc_final: 0.7919 (t) REVERT: B 301 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7035 (mp) REVERT: B 312 MET cc_start: 0.8600 (mmt) cc_final: 0.8250 (mmp) outliers start: 39 outliers final: 30 residues processed: 162 average time/residue: 0.1872 time to fit residues: 42.9405 Evaluate side-chains 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 56 PHE 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 231 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 301 LEU 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 526 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 66 TRP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 275 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 356 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 SER 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: 2.9990 chunk 75 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 HIS B 326 GLN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9018 Z= 0.241 Angle : 0.611 10.177 12188 Z= 0.308 Chirality : 0.042 0.193 1452 Planarity : 0.004 0.033 1542 Dihedral : 4.156 19.932 1248 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.20 % Allowed : 28.18 % Favored : 67.62 % 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: 1.91 (0.26), residues: 1142 helix: 2.10 (0.19), residues: 732 sheet: 0.95 (0.65), residues: 66 loop : -0.49 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 66 HIS 0.010 0.001 HIS A 405 PHE 0.019 0.002 PHE B 189 TYR 0.012 0.001 TYR A 162 ARG 0.004 0.000 ARG B 517 ********************** 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 169 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7993 (tpp) cc_final: 0.7570 (tmm) REVERT: A 56 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.7984 (m-10) REVERT: A 301 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7542 (mp) REVERT: B 200 MET cc_start: 0.5933 (tpt) cc_final: 0.5433 (tpt) REVERT: B 279 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 283 THR cc_start: 0.8489 (p) cc_final: 0.8068 (t) REVERT: B 301 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7113 (mp) outliers start: 41 outliers final: 34 residues processed: 161 average time/residue: 0.1877 time to fit residues: 43.0349 Evaluate side-chains 161 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 69 LEU 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 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 301 LEU 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 389 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 66 TRP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 LEU 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 321 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 390 THR Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 SER 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: 0.6980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 HIS B 326 GLN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.187281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 150)---------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154289 restraints weight = 10115.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150034 restraints weight = 13497.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150262 restraints weight = 11017.103| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9018 Z= 0.267 Angle : 0.935 59.200 12188 Z= 0.538 Chirality : 0.047 0.821 1452 Planarity : 0.004 0.072 1542 Dihedral : 4.189 21.016 1248 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.61 % Allowed : 27.97 % Favored : 67.42 % Cbeta Deviations : 0.09 % 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: 1.92 (0.26), residues: 1142 helix: 2.11 (0.19), residues: 732 sheet: 0.96 (0.65), residues: 66 loop : -0.49 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 66 HIS 0.008 0.001 HIS A 405 PHE 0.018 0.002 PHE B 189 TYR 0.011 0.001 TYR A 162 ARG 0.003 0.000 ARG B 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.67 seconds wall clock time: 34 minutes 51.85 seconds (2091.85 seconds total)