Starting phenix.real_space_refine on Wed Mar 4 05:59:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xuj_33471/03_2026/7xuj_33471.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xuj_33471/03_2026/7xuj_33471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xuj_33471/03_2026/7xuj_33471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xuj_33471/03_2026/7xuj_33471.map" model { file = "/net/cci-nas-00/data/ceres_data/7xuj_33471/03_2026/7xuj_33471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xuj_33471/03_2026/7xuj_33471.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 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 40 5.16 5 C 7486 2.51 5 N 1798 2.21 5 O 1972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11296 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5486 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 31, 'TRANS': 671} Chain breaks: 1 Chain: "B" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5486 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 31, 'TRANS': 671} Chain breaks: 1 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'I2R': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'I2R': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.66, per 1000 atoms: 0.24 Number of scatterers: 11296 At special positions: 0 Unit cell: (100.161, 123.855, 105.546, 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 40 16.00 O 1972 8.00 N 1798 7.00 C 7486 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 - 3.00 Amino acid : True - 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: 0.85 Conformation dependent library (CDL) restraints added in 462.6 milliseconds 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 62.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.668A pdb=" N ASN A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.630A pdb=" N LYS A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 72 through 95 removed outlier: 3.925A pdb=" N VAL A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.899A pdb=" N LEU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.652A pdb=" N LEU A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 Processing helix chain 'A' and resid 170 through 196 removed outlier: 3.551A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.606A pdb=" N LEU A 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.524A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 252 removed outlier: 3.545A pdb=" N LYS A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.556A pdb=" N THR A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 282 removed outlier: 3.738A pdb=" N GLN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.964A pdb=" N VAL A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 467 through 503 removed outlier: 6.849A pdb=" N LEU A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N GLY A 485 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 584 removed outlier: 3.625A pdb=" N GLN A 584 " --> pdb=" O LYS A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 618 removed outlier: 3.838A pdb=" N VAL A 615 " --> pdb=" O GLN A 612 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 618 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 676 Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.644A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 712 through 725 removed outlier: 3.722A pdb=" N ASP A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 25 removed outlier: 3.668A pdb=" N ASN B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.630A pdb=" N LYS B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 72 through 95 removed outlier: 3.925A pdb=" N VAL B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.900A pdb=" N LEU B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.653A pdb=" N LEU B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 Processing helix chain 'B' and resid 170 through 196 removed outlier: 3.552A pdb=" N VAL B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.606A pdb=" N LEU B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.524A pdb=" N ILE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.546A pdb=" N LYS B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.555A pdb=" N THR B 257 " --> pdb=" O ILE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 282 removed outlier: 3.739A pdb=" N GLN B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 339 through 366 removed outlier: 3.964A pdb=" N VAL B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 467 through 503 removed outlier: 6.849A pdb=" N LEU B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N GLY B 485 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 563 through 584 removed outlier: 3.625A pdb=" N GLN B 584 " --> pdb=" O LYS B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 618 removed outlier: 3.839A pdb=" N VAL B 615 " --> pdb=" O GLN B 612 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 676 Processing helix chain 'B' and resid 687 through 695 removed outlier: 3.643A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 698 No H-bonds generated for 'chain 'B' and resid 696 through 698' Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 712 through 725 removed outlier: 3.723A pdb=" N ASP B 725 " --> pdb=" O LEU B 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.637A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 13.036A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS A 536 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASP A 652 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.637A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 13.036A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1716 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: 1.78 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1764 1.27 - 1.40: 2742 1.40 - 1.54: 6638 1.54 - 1.67: 358 1.67 - 1.81: 60 Bond restraints: 11562 Sorted by residual: bond pdb=" C10 I2R A 801 " pdb=" C5 I2R A 801 " ideal model delta sigma weight residual 1.392 1.554 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" C10 I2R B 803 " pdb=" C5 I2R B 803 " ideal model delta sigma weight residual 1.392 1.554 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" C11 I2R A 801 " pdb=" C6 I2R A 801 " ideal model delta sigma weight residual 1.397 1.557 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C11 I2R B 803 " pdb=" C6 I2R B 803 " ideal model delta sigma weight residual 1.397 1.556 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" C17 I2R B 803 " pdb=" C20 I2R B 803 " ideal model delta sigma weight residual 1.389 1.533 -0.144 2.00e-02 2.50e+03 5.15e+01 ... (remaining 11557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 15480 3.06 - 6.13: 222 6.13 - 9.19: 30 9.19 - 12.25: 4 12.25 - 15.31: 2 Bond angle restraints: 15738 Sorted by residual: angle pdb=" CB GLU B 692 " pdb=" CG GLU B 692 " pdb=" CD GLU B 692 " ideal model delta sigma weight residual 112.60 122.38 -9.78 1.70e+00 3.46e-01 3.31e+01 angle pdb=" CB GLU A 692 " pdb=" CG GLU A 692 " pdb=" CD GLU A 692 " ideal model delta sigma weight residual 112.60 122.35 -9.75 1.70e+00 3.46e-01 3.29e+01 angle pdb=" CA GLU A 692 " pdb=" CB GLU A 692 " pdb=" CG GLU A 692 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA GLU B 692 " pdb=" CB GLU B 692 " pdb=" CG GLU B 692 " ideal model delta sigma weight residual 114.10 123.78 -9.68 2.00e+00 2.50e-01 2.34e+01 angle pdb=" C PRO B 287 " pdb=" N VAL B 288 " pdb=" CA VAL B 288 " ideal model delta sigma weight residual 122.13 130.42 -8.29 1.85e+00 2.92e-01 2.01e+01 ... (remaining 15733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 6418 15.26 - 30.51: 652 30.51 - 45.77: 158 45.77 - 61.03: 40 61.03 - 76.28: 6 Dihedral angle restraints: 7274 sinusoidal: 3200 harmonic: 4074 Sorted by residual: dihedral pdb=" CA THR A 238 " pdb=" C THR A 238 " pdb=" N ASP A 239 " pdb=" CA ASP A 239 " ideal model delta harmonic sigma weight residual -180.00 -154.53 -25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA THR B 238 " pdb=" C THR B 238 " pdb=" N ASP B 239 " pdb=" CA ASP B 239 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP B 239 " pdb=" C ASP B 239 " pdb=" N PRO B 240 " pdb=" CA PRO B 240 " ideal model delta harmonic sigma weight residual 180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 7271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1808 0.119 - 0.238: 64 0.238 - 0.356: 2 0.356 - 0.475: 0 0.475 - 0.594: 2 Chirality restraints: 1876 Sorted by residual: chirality pdb=" CB VAL B 288 " pdb=" CA VAL B 288 " pdb=" CG1 VAL B 288 " pdb=" CG2 VAL B 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.77e+00 chirality pdb=" CB VAL B 641 " pdb=" CA VAL B 641 " pdb=" CG1 VAL B 641 " pdb=" CG2 VAL B 641 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1873 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 590 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO A 591 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 590 " -0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 591 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 100 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO B 101 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " 0.035 5.00e-02 4.00e+02 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2767 2.79 - 3.32: 9916 3.32 - 3.84: 18134 3.84 - 4.37: 21637 4.37 - 4.90: 37355 Nonbonded interactions: 89809 Sorted by model distance: nonbonded pdb=" O LEU B 269 " pdb=" OG SER B 273 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A 269 " pdb=" OG SER A 273 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR B 365 " pdb=" OE2 GLU B 404 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A 365 " pdb=" OE2 GLU A 404 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR A 503 " pdb=" OH TYR A 545 " model vdw 2.313 3.040 ... (remaining 89804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 725 or resid 802 or resid 804 through 805)) selection = (chain 'B' and (resid 8 through 725 or resid 802 or resid 804 through 805)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.630 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:5.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.010 0.162 11562 Z= 0.452 Angle : 0.944 15.315 15738 Z= 0.514 Chirality : 0.057 0.594 1876 Planarity : 0.008 0.080 1920 Dihedral : 13.427 76.283 4642 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.82 % Allowed : 4.95 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.17), residues: 1398 helix: -2.21 (0.13), residues: 858 sheet: 1.05 (0.81), residues: 36 loop : -2.78 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 399 TYR 0.026 0.002 TYR B 9 PHE 0.027 0.002 PHE A 130 TRP 0.016 0.002 TRP B 63 HIS 0.007 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.01001 (11562) covalent geometry : angle 0.94403 (15738) hydrogen bonds : bond 0.15286 ( 588) hydrogen bonds : angle 6.09939 ( 1716) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.418 Fit side-chains REVERT: A 58 PHE cc_start: 0.7679 (m-80) cc_final: 0.7458 (m-80) REVERT: A 99 ASP cc_start: 0.7729 (t0) cc_final: 0.7476 (t0) REVERT: A 281 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.7119 (mmm-85) REVERT: B 58 PHE cc_start: 0.7611 (m-80) cc_final: 0.7407 (m-80) REVERT: B 99 ASP cc_start: 0.7858 (t0) cc_final: 0.7561 (t0) REVERT: B 281 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7069 (mmm-85) REVERT: B 612 GLN cc_start: 0.8532 (mt0) cc_final: 0.8164 (mt0) outliers start: 22 outliers final: 4 residues processed: 151 average time/residue: 0.5119 time to fit residues: 84.2345 Evaluate side-chains 94 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 273 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.076813 restraints weight = 15338.257| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.20 r_work: 0.2672 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11562 Z= 0.127 Angle : 0.609 15.727 15738 Z= 0.315 Chirality : 0.042 0.151 1876 Planarity : 0.005 0.068 1920 Dihedral : 8.062 94.506 2094 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.40 % Allowed : 8.50 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.22), residues: 1398 helix: -0.14 (0.17), residues: 880 sheet: 1.56 (0.82), residues: 36 loop : -2.20 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 312 TYR 0.010 0.001 TYR B 107 PHE 0.019 0.001 PHE B 627 TRP 0.012 0.001 TRP A 63 HIS 0.008 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00273 (11562) covalent geometry : angle 0.60855 (15738) hydrogen bonds : bond 0.04383 ( 588) hydrogen bonds : angle 4.17356 ( 1716) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.439 Fit side-chains REVERT: A 24 ASN cc_start: 0.9114 (m-40) cc_final: 0.8818 (m110) REVERT: A 58 PHE cc_start: 0.7426 (m-80) cc_final: 0.7132 (m-80) REVERT: A 281 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.7031 (mmm-85) REVERT: B 24 ASN cc_start: 0.9074 (m-40) cc_final: 0.8714 (m110) REVERT: B 58 PHE cc_start: 0.7526 (m-80) cc_final: 0.7242 (m-80) REVERT: B 99 ASP cc_start: 0.8610 (t0) cc_final: 0.8404 (t0) REVERT: B 281 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.7003 (mmm-85) REVERT: B 529 MET cc_start: 0.9121 (mmm) cc_final: 0.8870 (mmt) outliers start: 17 outliers final: 7 residues processed: 116 average time/residue: 0.5034 time to fit residues: 63.9763 Evaluate side-chains 101 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 628 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 95 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 70 optimal weight: 0.1980 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.075116 restraints weight = 15464.317| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.21 r_work: 0.2643 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11562 Z= 0.160 Angle : 0.608 15.786 15738 Z= 0.313 Chirality : 0.043 0.148 1876 Planarity : 0.004 0.065 1920 Dihedral : 7.369 58.687 2090 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.98 % Allowed : 9.08 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.23), residues: 1398 helix: 0.53 (0.18), residues: 876 sheet: 1.70 (0.82), residues: 36 loop : -1.90 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 312 TYR 0.011 0.001 TYR B 9 PHE 0.019 0.001 PHE A 130 TRP 0.013 0.001 TRP B 63 HIS 0.014 0.002 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00376 (11562) covalent geometry : angle 0.60799 (15738) hydrogen bonds : bond 0.04328 ( 588) hydrogen bonds : angle 3.94980 ( 1716) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.330 Fit side-chains REVERT: A 38 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.7317 (m-70) REVERT: A 58 PHE cc_start: 0.7494 (m-80) cc_final: 0.7194 (m-80) REVERT: A 281 ARG cc_start: 0.7418 (ttm-80) cc_final: 0.7012 (mmm-85) REVERT: B 24 ASN cc_start: 0.9089 (m-40) cc_final: 0.8714 (m110) REVERT: B 38 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7305 (m-70) REVERT: B 58 PHE cc_start: 0.7571 (m-80) cc_final: 0.7285 (m-80) REVERT: B 281 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.7056 (mmm-85) REVERT: B 529 MET cc_start: 0.9133 (mmm) cc_final: 0.8877 (mmt) outliers start: 24 outliers final: 13 residues processed: 115 average time/residue: 0.4835 time to fit residues: 61.4605 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 129 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.075170 restraints weight = 15571.076| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.22 r_work: 0.2649 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11562 Z= 0.160 Angle : 0.608 15.786 15738 Z= 0.313 Chirality : 0.043 0.148 1876 Planarity : 0.004 0.065 1920 Dihedral : 7.794 118.116 2090 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.24 % Allowed : 11.22 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.23), residues: 1398 helix: 0.53 (0.18), residues: 876 sheet: 1.70 (0.82), residues: 36 loop : -1.90 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 312 TYR 0.011 0.001 TYR B 9 PHE 0.019 0.001 PHE A 130 TRP 0.013 0.001 TRP B 63 HIS 0.014 0.002 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00376 (11562) covalent geometry : angle 0.60799 (15738) hydrogen bonds : bond 0.04328 ( 588) hydrogen bonds : angle 3.94980 ( 1716) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.312 Fit side-chains REVERT: A 38 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7313 (m-70) REVERT: A 58 PHE cc_start: 0.7506 (m-80) cc_final: 0.7207 (m-80) REVERT: A 281 ARG cc_start: 0.7418 (ttm-80) cc_final: 0.7012 (mmm-85) REVERT: B 24 ASN cc_start: 0.9092 (m-40) cc_final: 0.8719 (m110) REVERT: B 38 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7303 (m-70) REVERT: B 58 PHE cc_start: 0.7575 (m-80) cc_final: 0.7289 (m-80) REVERT: B 281 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7056 (mmm-85) REVERT: B 529 MET cc_start: 0.9128 (mmm) cc_final: 0.8870 (mmt) outliers start: 15 outliers final: 13 residues processed: 101 average time/residue: 0.5255 time to fit residues: 58.0232 Evaluate side-chains 106 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.111304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.074372 restraints weight = 15629.332| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.22 r_work: 0.2632 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11562 Z= 0.183 Angle : 0.622 16.996 15738 Z= 0.318 Chirality : 0.044 0.144 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.659 97.356 2090 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.73 % Allowed : 11.30 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.23), residues: 1398 helix: 0.83 (0.18), residues: 876 sheet: 1.89 (0.80), residues: 36 loop : -1.76 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.013 0.001 TYR B 9 PHE 0.019 0.001 PHE A 130 TRP 0.014 0.001 TRP B 63 HIS 0.004 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00441 (11562) covalent geometry : angle 0.62156 (15738) hydrogen bonds : bond 0.04427 ( 588) hydrogen bonds : angle 3.87847 ( 1716) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.480 Fit side-chains REVERT: A 38 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7349 (m-70) REVERT: A 48 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7741 (mp10) REVERT: A 58 PHE cc_start: 0.7546 (m-80) cc_final: 0.7255 (m-80) REVERT: A 281 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.7071 (mmm-85) REVERT: B 24 ASN cc_start: 0.9096 (m-40) cc_final: 0.8733 (m110) REVERT: B 38 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7411 (m-70) REVERT: B 58 PHE cc_start: 0.7642 (m-80) cc_final: 0.7365 (m-80) REVERT: B 70 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8653 (tppp) REVERT: B 281 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.7103 (mmm-85) REVERT: B 468 ASP cc_start: 0.8578 (m-30) cc_final: 0.8348 (m-30) outliers start: 21 outliers final: 14 residues processed: 107 average time/residue: 0.4779 time to fit residues: 56.4926 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 0.0170 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.074445 restraints weight = 15606.551| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.21 r_work: 0.2633 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11562 Z= 0.176 Angle : 0.620 17.013 15738 Z= 0.317 Chirality : 0.044 0.142 1876 Planarity : 0.004 0.063 1920 Dihedral : 8.031 118.094 2090 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.32 % Allowed : 12.46 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1398 helix: 0.84 (0.18), residues: 876 sheet: 1.89 (0.80), residues: 36 loop : -1.76 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.013 0.001 TYR B 9 PHE 0.019 0.001 PHE A 130 TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00428 (11562) covalent geometry : angle 0.61978 (15738) hydrogen bonds : bond 0.04388 ( 588) hydrogen bonds : angle 3.87953 ( 1716) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.489 Fit side-chains REVERT: A 38 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.7350 (m-70) REVERT: A 48 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7739 (mp10) REVERT: A 58 PHE cc_start: 0.7545 (m-80) cc_final: 0.7253 (m-80) REVERT: A 281 ARG cc_start: 0.7478 (ttm-80) cc_final: 0.7063 (mmm-85) REVERT: B 24 ASN cc_start: 0.9097 (m-40) cc_final: 0.8733 (m110) REVERT: B 38 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7411 (m-70) REVERT: B 58 PHE cc_start: 0.7642 (m-80) cc_final: 0.7364 (m-80) REVERT: B 70 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8652 (tppp) REVERT: B 281 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.7090 (mmm-85) REVERT: B 468 ASP cc_start: 0.8579 (m-30) cc_final: 0.8349 (m-30) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.4894 time to fit residues: 54.0359 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 66 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 116 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.074482 restraints weight = 15511.292| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.21 r_work: 0.2633 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11562 Z= 0.176 Angle : 0.621 17.015 15738 Z= 0.317 Chirality : 0.044 0.141 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.844 118.114 2090 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.40 % Allowed : 12.29 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1398 helix: 0.84 (0.18), residues: 876 sheet: 1.89 (0.80), residues: 36 loop : -1.76 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.013 0.001 TYR B 9 PHE 0.019 0.001 PHE A 130 TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00427 (11562) covalent geometry : angle 0.62097 (15738) hydrogen bonds : bond 0.04386 ( 588) hydrogen bonds : angle 3.87962 ( 1716) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.371 Fit side-chains REVERT: A 38 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7359 (m-70) REVERT: A 48 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7739 (mp10) REVERT: A 58 PHE cc_start: 0.7545 (m-80) cc_final: 0.7254 (m-80) REVERT: A 281 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7068 (mmm-85) REVERT: B 24 ASN cc_start: 0.9093 (m-40) cc_final: 0.8729 (m110) REVERT: B 38 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7418 (m-70) REVERT: B 58 PHE cc_start: 0.7643 (m-80) cc_final: 0.7364 (m-80) REVERT: B 70 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8652 (tppp) REVERT: B 281 ARG cc_start: 0.7469 (ttm-80) cc_final: 0.7095 (mmm-85) REVERT: B 468 ASP cc_start: 0.8582 (m-30) cc_final: 0.8352 (m-30) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 0.4651 time to fit residues: 51.2958 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 90 optimal weight: 0.0060 chunk 15 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 124 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.074974 restraints weight = 15504.129| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.21 r_work: 0.2638 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11562 Z= 0.134 Angle : 0.625 17.956 15738 Z= 0.319 Chirality : 0.043 0.149 1876 Planarity : 0.004 0.062 1920 Dihedral : 7.771 115.767 2090 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.40 % Allowed : 11.96 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1398 helix: 0.99 (0.19), residues: 876 sheet: 1.88 (0.80), residues: 36 loop : -1.71 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.010 0.001 TYR A 9 PHE 0.018 0.001 PHE A 130 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00298 (11562) covalent geometry : angle 0.62454 (15738) hydrogen bonds : bond 0.04224 ( 588) hydrogen bonds : angle 3.86003 ( 1716) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.395 Fit side-chains REVERT: A 38 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7326 (m-70) REVERT: A 48 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7692 (mp10) REVERT: A 58 PHE cc_start: 0.7436 (m-80) cc_final: 0.7148 (m-80) REVERT: A 281 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7142 (mmm-85) REVERT: B 24 ASN cc_start: 0.9086 (m-40) cc_final: 0.8681 (m110) REVERT: B 38 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7391 (m-70) REVERT: B 58 PHE cc_start: 0.7522 (m-80) cc_final: 0.7234 (m-80) REVERT: B 281 ARG cc_start: 0.7464 (ttm-80) cc_final: 0.7092 (mmm-85) REVERT: B 468 ASP cc_start: 0.8542 (m-30) cc_final: 0.8295 (m-30) outliers start: 17 outliers final: 16 residues processed: 103 average time/residue: 0.4469 time to fit residues: 50.9368 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 61 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 0.2980 chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.075028 restraints weight = 15374.392| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.20 r_work: 0.2640 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11562 Z= 0.134 Angle : 0.624 17.956 15738 Z= 0.319 Chirality : 0.043 0.149 1876 Planarity : 0.004 0.062 1920 Dihedral : 7.789 118.116 2090 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.49 % Allowed : 12.13 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1398 helix: 0.99 (0.19), residues: 876 sheet: 1.88 (0.80), residues: 36 loop : -1.71 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.010 0.001 TYR A 9 PHE 0.018 0.001 PHE A 130 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00299 (11562) covalent geometry : angle 0.62449 (15738) hydrogen bonds : bond 0.04224 ( 588) hydrogen bonds : angle 3.86002 ( 1716) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.459 Fit side-chains REVERT: A 38 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7328 (m-70) REVERT: A 48 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7693 (mp10) REVERT: A 58 PHE cc_start: 0.7434 (m-80) cc_final: 0.7146 (m-80) REVERT: A 281 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7141 (mmm-85) REVERT: B 24 ASN cc_start: 0.9087 (m-40) cc_final: 0.8682 (m110) REVERT: B 38 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7395 (m-70) REVERT: B 58 PHE cc_start: 0.7516 (m-80) cc_final: 0.7229 (m-80) REVERT: B 281 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.7092 (mmm-85) REVERT: B 468 ASP cc_start: 0.8540 (m-30) cc_final: 0.8294 (m-30) outliers start: 18 outliers final: 16 residues processed: 101 average time/residue: 0.4667 time to fit residues: 51.9469 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 106 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.074989 restraints weight = 15474.134| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.21 r_work: 0.2639 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11562 Z= 0.134 Angle : 0.624 17.956 15738 Z= 0.319 Chirality : 0.043 0.149 1876 Planarity : 0.004 0.062 1920 Dihedral : 7.789 118.116 2090 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.49 % Allowed : 12.13 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1398 helix: 0.99 (0.19), residues: 876 sheet: 1.88 (0.80), residues: 36 loop : -1.71 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.010 0.001 TYR A 9 PHE 0.018 0.001 PHE A 130 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00299 (11562) covalent geometry : angle 0.62449 (15738) hydrogen bonds : bond 0.04224 ( 588) hydrogen bonds : angle 3.86002 ( 1716) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2796 Ramachandran restraints generated. 1398 Oldfield, 0 Emsley, 1398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.439 Fit side-chains REVERT: A 38 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7327 (m-70) REVERT: A 48 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7693 (mp10) REVERT: A 58 PHE cc_start: 0.7435 (m-80) cc_final: 0.7147 (m-80) REVERT: A 281 ARG cc_start: 0.7533 (ttm-80) cc_final: 0.7142 (mmm-85) REVERT: B 24 ASN cc_start: 0.9087 (m-40) cc_final: 0.8683 (m110) REVERT: B 38 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7395 (m-70) REVERT: B 58 PHE cc_start: 0.7517 (m-80) cc_final: 0.7230 (m-80) REVERT: B 281 ARG cc_start: 0.7464 (ttm-80) cc_final: 0.7093 (mmm-85) REVERT: B 468 ASP cc_start: 0.8541 (m-30) cc_final: 0.8295 (m-30) outliers start: 18 outliers final: 16 residues processed: 101 average time/residue: 0.4681 time to fit residues: 52.1733 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 628 HIS Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 67 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.074981 restraints weight = 15483.549| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.21 r_work: 0.2639 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11562 Z= 0.134 Angle : 0.624 17.956 15738 Z= 0.319 Chirality : 0.043 0.149 1876 Planarity : 0.004 0.062 1920 Dihedral : 7.789 118.116 2090 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.49 % Allowed : 12.13 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1398 helix: 0.99 (0.19), residues: 876 sheet: 1.88 (0.80), residues: 36 loop : -1.71 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.010 0.001 TYR A 9 PHE 0.018 0.001 PHE A 130 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00299 (11562) covalent geometry : angle 0.62449 (15738) hydrogen bonds : bond 0.04224 ( 588) hydrogen bonds : angle 3.86002 ( 1716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3578.14 seconds wall clock time: 61 minutes 49.61 seconds (3709.61 seconds total)