Starting phenix.real_space_refine on Sun Mar 17 14:00:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/03_2024/6vqu_21357.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/03_2024/6vqu_21357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/03_2024/6vqu_21357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/03_2024/6vqu_21357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/03_2024/6vqu_21357.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqu_21357/03_2024/6vqu_21357.pdb" } resolution = 3.88 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= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8895 atoms to isotropic. 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 24 5.16 5 C 5846 2.51 5 N 1624 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A ASP 468": "OD1" <-> "OD2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B ASP 468": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B GLU 523": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9156 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4578 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 15, 'TRANS': 573} Chain: "B" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4578 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 15, 'TRANS': 573} Time building chain proxies: 5.02, per 1000 atoms: 0.55 Number of scatterers: 9156 At special positions: 0 Unit cell: (110.922, 86.736, 140.946, 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 24 16.00 O 1662 8.00 N 1624 7.00 C 5846 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: 3.49 Conformation dependent library (CDL) restraints added in 1.7 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 73.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 32 through 69 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 75 through 127 removed outlier: 4.534A pdb=" N ARG A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.878A pdb=" N HIS A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 161 Processing helix chain 'A' and resid 161 through 178 Processing helix chain 'A' and resid 181 through 230 removed outlier: 3.962A pdb=" N VAL A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 239 through 293 Processing helix chain 'A' and resid 298 through 312 removed outlier: 4.021A pdb=" N VAL A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.929A pdb=" N ASP A 316 " --> pdb=" O ARG A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 317 through 341 Processing helix chain 'A' and resid 401 through 408 removed outlier: 4.535A pdb=" N ARG A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.546A pdb=" N THR A 489 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 529 through 544 removed outlier: 4.389A pdb=" N SER A 538 " --> pdb=" O GLN A 534 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 587 through 602 Processing helix chain 'B' and resid 15 through 28 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 32 through 69 Proline residue: B 57 - end of helix Processing helix chain 'B' and resid 75 through 127 removed outlier: 4.533A pdb=" N ARG B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.879A pdb=" N HIS B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 161 Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'B' and resid 181 through 230 removed outlier: 3.962A pdb=" N VAL B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 239 through 293 Processing helix chain 'B' and resid 298 through 312 removed outlier: 4.020A pdb=" N VAL B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 316 removed outlier: 3.928A pdb=" N ASP B 316 " --> pdb=" O ARG B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 317 through 341 Processing helix chain 'B' and resid 401 through 408 removed outlier: 4.535A pdb=" N ARG B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 463 through 474 Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 485 through 489 removed outlier: 3.546A pdb=" N THR B 489 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 529 through 544 removed outlier: 4.389A pdb=" N SER B 538 " --> pdb=" O GLN B 534 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 539 " --> pdb=" O ASP B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 587 through 602 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 384 removed outlier: 4.166A pdb=" N GLY A 379 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL A 366 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER A 381 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP A 364 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU A 383 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR A 362 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE A 363 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 419 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN A 365 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG A 417 " --> pdb=" O ASN A 365 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 440 removed outlier: 6.724A pdb=" N GLY A 438 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP A 522 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 440 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 519 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG A 389 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU A 566 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA A 391 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A 568 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 393 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP A 569 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 377 through 384 removed outlier: 4.166A pdb=" N GLY B 379 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL B 366 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER B 381 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 364 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU B 383 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B 362 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE B 363 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 419 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN B 365 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG B 417 " --> pdb=" O ASN B 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 437 through 440 removed outlier: 6.725A pdb=" N GLY B 438 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP B 522 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 440 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU B 519 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE B 552 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE B 521 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARG B 389 " --> pdb=" O THR B 564 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU B 566 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA B 391 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B 568 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 393 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP B 569 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1962 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: 2.84 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2965 1.34 - 1.45: 1418 1.45 - 1.57: 4895 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 9326 Sorted by residual: bond pdb=" CB PRO B 57 " pdb=" CG PRO B 57 " ideal model delta sigma weight residual 1.492 1.384 0.108 5.00e-02 4.00e+02 4.68e+00 bond pdb=" CB PRO A 57 " pdb=" CG PRO A 57 " ideal model delta sigma weight residual 1.492 1.384 0.108 5.00e-02 4.00e+02 4.66e+00 bond pdb=" C GLN B 74 " pdb=" N PRO B 75 " ideal model delta sigma weight residual 1.334 1.381 -0.048 2.34e-02 1.83e+03 4.13e+00 bond pdb=" C GLN A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.08e+00 bond pdb=" CA LEU A 56 " pdb=" C LEU A 56 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.26e-02 6.30e+03 3.47e+00 ... (remaining 9321 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.91: 142 105.91 - 112.93: 5135 112.93 - 119.94: 3197 119.94 - 126.96: 4094 126.96 - 133.98: 100 Bond angle restraints: 12668 Sorted by residual: angle pdb=" CA ARG A 494 " pdb=" CB ARG A 494 " pdb=" CG ARG A 494 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CA ARG B 494 " pdb=" CB ARG B 494 " pdb=" CG ARG B 494 " ideal model delta sigma weight residual 114.10 121.36 -7.26 2.00e+00 2.50e-01 1.32e+01 angle pdb=" C ASP B 569 " pdb=" N GLN B 570 " pdb=" CA GLN B 570 " ideal model delta sigma weight residual 122.46 127.56 -5.10 1.41e+00 5.03e-01 1.31e+01 angle pdb=" C ASP A 569 " pdb=" N GLN A 570 " pdb=" CA GLN A 570 " ideal model delta sigma weight residual 122.46 127.49 -5.03 1.41e+00 5.03e-01 1.27e+01 angle pdb=" C GLU B 493 " pdb=" N ARG B 494 " pdb=" CA ARG B 494 " ideal model delta sigma weight residual 122.08 127.09 -5.01 1.47e+00 4.63e-01 1.16e+01 ... (remaining 12663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.89: 4673 13.89 - 27.78: 621 27.78 - 41.66: 174 41.66 - 55.55: 50 55.55 - 69.44: 18 Dihedral angle restraints: 5536 sinusoidal: 2140 harmonic: 3396 Sorted by residual: dihedral pdb=" CA PHE A 368 " pdb=" C PHE A 368 " pdb=" N GLY A 369 " pdb=" CA GLY A 369 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PHE B 368 " pdb=" C PHE B 368 " pdb=" N GLY B 369 " pdb=" CA GLY B 369 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ALA A 76 " pdb=" C ALA A 76 " pdb=" N LEU A 77 " pdb=" CA LEU A 77 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1079 0.053 - 0.106: 279 0.106 - 0.160: 111 0.160 - 0.213: 9 0.213 - 0.266: 6 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CB VAL B 543 " pdb=" CA VAL B 543 " pdb=" CG1 VAL B 543 " pdb=" CG2 VAL B 543 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL A 543 " pdb=" CA VAL A 543 " pdb=" CG1 VAL A 543 " pdb=" CG2 VAL A 543 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE A 559 " pdb=" CA ILE A 559 " pdb=" CG1 ILE A 559 " pdb=" CG2 ILE A 559 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1481 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 543 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C VAL A 543 " -0.063 2.00e-02 2.50e+03 pdb=" O VAL A 543 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA A 544 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 543 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C VAL B 543 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL B 543 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA B 544 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 303 " 0.024 2.00e-02 2.50e+03 1.70e-02 5.03e+00 pdb=" CG PHE A 303 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 303 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 303 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 303 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 303 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 303 " 0.013 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2554 2.80 - 3.33: 9066 3.33 - 3.85: 15907 3.85 - 4.38: 17055 4.38 - 4.90: 28934 Nonbonded interactions: 73516 Sorted by model distance: nonbonded pdb=" O THR A 199 " pdb=" OG1 THR A 203 " model vdw 2.276 2.440 nonbonded pdb=" O THR B 199 " pdb=" OG1 THR B 203 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR B 429 " pdb=" OG SER B 432 " model vdw 2.293 2.440 nonbonded pdb=" O ASP B 15 " pdb=" OG1 THR B 19 " model vdw 2.293 2.440 nonbonded pdb=" O ASP A 15 " pdb=" OG1 THR A 19 " model vdw 2.293 2.440 ... (remaining 73511 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: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.000 Extract box with map and model: 13.370 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.030 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 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 : 0.007 0.108 9326 Z= 0.438 Angle : 0.942 8.779 12668 Z= 0.539 Chirality : 0.056 0.266 1484 Planarity : 0.007 0.054 1616 Dihedral : 14.622 69.440 3352 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.70 % Allowed : 8.09 % Favored : 90.21 % 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: -2.26 (0.21), residues: 1174 helix: -1.29 (0.15), residues: 788 sheet: -1.53 (0.62), residues: 72 loop : -1.51 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 28 HIS 0.005 0.001 HIS B 125 PHE 0.035 0.003 PHE B 303 TYR 0.018 0.003 TYR A 60 ARG 0.016 0.001 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.9435 (tmm) cc_final: 0.9034 (tmm) REVERT: A 592 MET cc_start: 0.9194 (mtp) cc_final: 0.8905 (mtp) REVERT: B 154 MET cc_start: 0.9437 (tmm) cc_final: 0.9124 (tmm) REVERT: B 592 MET cc_start: 0.9240 (mtp) cc_final: 0.8992 (mtp) outliers start: 16 outliers final: 2 residues processed: 74 average time/residue: 0.2784 time to fit residues: 27.5897 Evaluate side-chains 41 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 543 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.0170 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 125 HIS A 504 GLN B 14 HIS B 74 GLN B 119 ASN B 125 HIS B 504 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9326 Z= 0.155 Angle : 0.565 7.566 12668 Z= 0.297 Chirality : 0.038 0.144 1484 Planarity : 0.005 0.109 1616 Dihedral : 4.128 20.505 1308 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.23 % Allowed : 11.91 % Favored : 85.85 % 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: 0.30 (0.23), residues: 1174 helix: 0.82 (0.17), residues: 798 sheet: -1.27 (0.61), residues: 72 loop : -0.89 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 291 HIS 0.003 0.001 HIS B 125 PHE 0.021 0.001 PHE A 105 TYR 0.011 0.001 TYR A 195 ARG 0.011 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 48 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.9457 (tmm) cc_final: 0.9056 (tmm) REVERT: A 320 MET cc_start: 0.9134 (ptp) cc_final: 0.8809 (pmm) REVERT: A 592 MET cc_start: 0.9127 (mtp) cc_final: 0.8859 (mtp) REVERT: B 154 MET cc_start: 0.9472 (tmm) cc_final: 0.9141 (tmm) REVERT: B 335 MET cc_start: 0.9317 (mpp) cc_final: 0.9097 (mpp) REVERT: B 592 MET cc_start: 0.9181 (mtp) cc_final: 0.8946 (mtp) outliers start: 21 outliers final: 9 residues processed: 67 average time/residue: 0.2064 time to fit residues: 20.3235 Evaluate side-chains 43 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 543 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 74 GLN A 119 ASN A 125 HIS B 119 ASN B 125 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9326 Z= 0.174 Angle : 0.543 8.558 12668 Z= 0.287 Chirality : 0.038 0.142 1484 Planarity : 0.003 0.035 1616 Dihedral : 3.790 21.744 1307 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.45 % Allowed : 14.04 % Favored : 83.51 % 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: 1.46 (0.24), residues: 1174 helix: 1.74 (0.18), residues: 796 sheet: -1.13 (0.60), residues: 72 loop : -0.46 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 291 HIS 0.003 0.001 HIS B 378 PHE 0.022 0.001 PHE B 105 TYR 0.009 0.001 TYR A 195 ARG 0.004 0.000 ARG A 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 36 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.9477 (tmm) cc_final: 0.9061 (tmm) REVERT: A 159 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9408 (tt) REVERT: A 320 MET cc_start: 0.9123 (ptp) cc_final: 0.8832 (pmm) REVERT: A 592 MET cc_start: 0.9107 (mtp) cc_final: 0.8842 (mtp) REVERT: B 154 MET cc_start: 0.9502 (tmm) cc_final: 0.9162 (tmm) REVERT: B 159 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9399 (tt) REVERT: B 284 MET cc_start: 0.9216 (mtt) cc_final: 0.8998 (mtt) REVERT: B 335 MET cc_start: 0.9279 (mpp) cc_final: 0.9060 (mpp) REVERT: B 592 MET cc_start: 0.9205 (mtp) cc_final: 0.8960 (mtp) outliers start: 23 outliers final: 9 residues processed: 58 average time/residue: 0.1767 time to fit residues: 15.7188 Evaluate side-chains 45 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 0.0770 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 125 HIS B 119 ASN B 125 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9326 Z= 0.175 Angle : 0.540 7.290 12668 Z= 0.282 Chirality : 0.039 0.167 1484 Planarity : 0.003 0.023 1616 Dihedral : 3.717 22.464 1306 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.45 % Allowed : 15.74 % Favored : 81.81 % 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: 1.86 (0.24), residues: 1174 helix: 1.98 (0.18), residues: 800 sheet: -0.98 (0.61), residues: 72 loop : -0.15 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 17 HIS 0.003 0.000 HIS A 125 PHE 0.022 0.001 PHE A 105 TYR 0.010 0.001 TYR A 195 ARG 0.015 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 32 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9460 (tmm) cc_final: 0.9132 (tmm) REVERT: A 159 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9317 (tt) REVERT: A 592 MET cc_start: 0.9108 (mtp) cc_final: 0.8838 (mtp) REVERT: B 154 MET cc_start: 0.9503 (tmm) cc_final: 0.9150 (tmm) REVERT: B 159 LEU cc_start: 0.9700 (OUTLIER) cc_final: 0.9369 (tt) REVERT: B 592 MET cc_start: 0.9204 (mtp) cc_final: 0.8950 (mtp) outliers start: 23 outliers final: 15 residues processed: 55 average time/residue: 0.1665 time to fit residues: 15.2400 Evaluate side-chains 48 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 31 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.0170 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 125 HIS A 442 GLN B 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9326 Z= 0.190 Angle : 0.542 9.919 12668 Z= 0.282 Chirality : 0.039 0.169 1484 Planarity : 0.003 0.022 1616 Dihedral : 3.645 16.501 1306 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.66 % Allowed : 16.70 % Favored : 80.64 % 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: 2.11 (0.25), residues: 1174 helix: 2.12 (0.18), residues: 800 sheet: -0.80 (0.62), residues: 72 loop : 0.09 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 17 HIS 0.003 0.001 HIS A 125 PHE 0.022 0.001 PHE A 105 TYR 0.009 0.001 TYR A 195 ARG 0.002 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 31 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.9499 (tmm) cc_final: 0.9158 (tmm) REVERT: A 159 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9425 (tt) REVERT: A 592 MET cc_start: 0.9115 (mtp) cc_final: 0.8837 (mtp) REVERT: B 154 MET cc_start: 0.9496 (tmm) cc_final: 0.9112 (tmm) REVERT: B 159 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9377 (tt) REVERT: B 335 MET cc_start: 0.9254 (mpp) cc_final: 0.8959 (mpp) REVERT: B 592 MET cc_start: 0.9187 (mtp) cc_final: 0.8907 (mtp) outliers start: 25 outliers final: 13 residues processed: 55 average time/residue: 0.1590 time to fit residues: 14.6230 Evaluate side-chains 46 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 31 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 0.0270 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 overall best weight: 1.9242 ------------------------------------------------------------------------------- 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: 0.8708 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9326 Z= 0.208 Angle : 0.558 11.217 12668 Z= 0.289 Chirality : 0.039 0.170 1484 Planarity : 0.003 0.024 1616 Dihedral : 3.665 16.569 1306 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.55 % Allowed : 16.91 % Favored : 80.53 % 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: 2.15 (0.25), residues: 1174 helix: 2.16 (0.18), residues: 802 sheet: -0.60 (0.62), residues: 72 loop : 0.01 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 17 HIS 0.003 0.001 HIS A 125 PHE 0.018 0.001 PHE A 105 TYR 0.009 0.001 TYR A 195 ARG 0.003 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 31 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9520 (tmm) cc_final: 0.9177 (tmm) REVERT: A 159 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9410 (tt) REVERT: A 592 MET cc_start: 0.9128 (mtp) cc_final: 0.8833 (mtp) REVERT: B 154 MET cc_start: 0.9533 (tmm) cc_final: 0.9168 (tmm) REVERT: B 159 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9414 (tt) REVERT: B 307 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7454 (t80) REVERT: B 592 MET cc_start: 0.9192 (mtp) cc_final: 0.8880 (mtp) outliers start: 24 outliers final: 17 residues processed: 54 average time/residue: 0.1561 time to fit residues: 13.8774 Evaluate side-chains 51 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 31 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9326 Z= 0.166 Angle : 0.553 13.359 12668 Z= 0.279 Chirality : 0.039 0.172 1484 Planarity : 0.003 0.023 1616 Dihedral : 3.639 18.230 1306 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.66 % Allowed : 17.66 % Favored : 79.68 % 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: 2.26 (0.25), residues: 1174 helix: 2.19 (0.18), residues: 800 sheet: -0.53 (0.63), residues: 72 loop : 0.23 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 17 HIS 0.003 0.001 HIS A 125 PHE 0.016 0.001 PHE B 105 TYR 0.010 0.001 TYR A 195 ARG 0.003 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 35 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9510 (tmm) cc_final: 0.9169 (tmm) REVERT: A 159 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9459 (tt) REVERT: A 592 MET cc_start: 0.9126 (mtp) cc_final: 0.8817 (mtp) REVERT: B 154 MET cc_start: 0.9506 (tmm) cc_final: 0.9208 (tmm) REVERT: B 159 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9392 (tt) REVERT: B 592 MET cc_start: 0.9175 (mtp) cc_final: 0.8852 (mtp) outliers start: 25 outliers final: 16 residues processed: 59 average time/residue: 0.1993 time to fit residues: 17.4906 Evaluate side-chains 51 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 33 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.0870 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9326 Z= 0.152 Angle : 0.588 12.035 12668 Z= 0.289 Chirality : 0.039 0.186 1484 Planarity : 0.003 0.049 1616 Dihedral : 3.648 20.527 1306 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.91 % Allowed : 18.19 % Favored : 79.89 % 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: 2.29 (0.25), residues: 1174 helix: 2.21 (0.18), residues: 800 sheet: -0.53 (0.62), residues: 72 loop : 0.24 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 291 HIS 0.003 0.000 HIS A 125 PHE 0.032 0.001 PHE B 157 TYR 0.010 0.001 TYR A 195 ARG 0.011 0.000 ARG A 531 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 37 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9480 (tmm) cc_final: 0.9141 (tmm) REVERT: A 159 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9454 (tt) REVERT: A 592 MET cc_start: 0.9111 (mtp) cc_final: 0.8792 (mtp) REVERT: B 154 MET cc_start: 0.9513 (tmm) cc_final: 0.9222 (tmm) REVERT: B 159 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9392 (tt) REVERT: B 592 MET cc_start: 0.9159 (mtp) cc_final: 0.8832 (mtp) outliers start: 18 outliers final: 13 residues processed: 54 average time/residue: 0.1694 time to fit residues: 14.5208 Evaluate side-chains 50 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 35 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9326 Z= 0.183 Angle : 0.596 11.338 12668 Z= 0.298 Chirality : 0.039 0.189 1484 Planarity : 0.003 0.044 1616 Dihedral : 3.689 21.075 1306 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.81 % Allowed : 18.40 % Favored : 79.79 % 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: 2.26 (0.25), residues: 1174 helix: 2.17 (0.18), residues: 800 sheet: -0.41 (0.63), residues: 70 loop : 0.27 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 17 HIS 0.003 0.000 HIS A 125 PHE 0.023 0.001 PHE B 157 TYR 0.013 0.001 TYR A 457 ARG 0.010 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 37 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.9503 (tmm) cc_final: 0.9159 (tmm) REVERT: A 159 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9471 (tt) REVERT: A 592 MET cc_start: 0.9115 (mtp) cc_final: 0.8799 (mtp) REVERT: B 154 MET cc_start: 0.9512 (tmm) cc_final: 0.9220 (tmm) REVERT: B 159 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9436 (tt) REVERT: B 335 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8774 (mpp) REVERT: B 592 MET cc_start: 0.9146 (mtp) cc_final: 0.8818 (mtp) outliers start: 17 outliers final: 13 residues processed: 51 average time/residue: 0.1789 time to fit residues: 14.4860 Evaluate side-chains 52 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 56 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 chunk 28 optimal weight: 5.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9326 Z= 0.156 Angle : 0.614 11.757 12668 Z= 0.305 Chirality : 0.039 0.195 1484 Planarity : 0.003 0.038 1616 Dihedral : 3.658 21.985 1306 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.91 % Allowed : 19.04 % Favored : 79.04 % 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: 2.25 (0.25), residues: 1174 helix: 2.18 (0.18), residues: 794 sheet: -0.27 (0.63), residues: 70 loop : 0.19 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 291 HIS 0.003 0.000 HIS A 125 PHE 0.023 0.001 PHE B 336 TYR 0.013 0.001 TYR A 457 ARG 0.010 0.000 ARG B 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.9482 (tmm) cc_final: 0.9153 (tmm) REVERT: A 159 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9491 (tt) REVERT: A 335 MET cc_start: 0.9289 (mpp) cc_final: 0.9026 (mpp) REVERT: A 592 MET cc_start: 0.9115 (mtp) cc_final: 0.8791 (mtp) REVERT: B 154 MET cc_start: 0.9487 (tmm) cc_final: 0.9187 (tmm) REVERT: B 159 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9426 (tt) REVERT: B 512 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9118 (mm) REVERT: B 592 MET cc_start: 0.9139 (mtp) cc_final: 0.8801 (mtp) outliers start: 18 outliers final: 13 residues processed: 57 average time/residue: 0.1826 time to fit residues: 16.5969 Evaluate side-chains 53 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 540 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 442 GLN B 125 HIS B 442 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.034275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.025800 restraints weight = 87996.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.026679 restraints weight = 53384.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.027293 restraints weight = 38483.707| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9326 Z= 0.247 Angle : 0.660 11.564 12668 Z= 0.334 Chirality : 0.040 0.204 1484 Planarity : 0.003 0.042 1616 Dihedral : 3.785 21.323 1306 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.49 % Allowed : 19.79 % Favored : 78.72 % 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: 2.20 (0.25), residues: 1174 helix: 2.11 (0.18), residues: 794 sheet: -0.43 (0.63), residues: 72 loop : 0.32 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 28 HIS 0.003 0.001 HIS A 125 PHE 0.023 0.002 PHE B 157 TYR 0.012 0.001 TYR A 457 ARG 0.009 0.001 ARG B 531 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1646.72 seconds wall clock time: 30 minutes 55.66 seconds (1855.66 seconds total)