Starting phenix.real_space_refine on Fri Jul 3 01:21:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xuj_33471/07_2026/7xuj_33471.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xuj_33471/07_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_33471/07_2026/7xuj_33471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xuj_33471/07_2026/7xuj_33471.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xuj_33471/07_2026/7xuj_33471.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xuj_33471/07_2026/7xuj_33471.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xuj_33471/07_2026/7xuj_33471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xuj_33471/07_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-6108/lib/python3.11/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: 2.84, per 1000 atoms: 0.25 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: 1.05 Conformation dependent library (CDL) restraints added in 596.5 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: 0.34 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: 1.87 Time building geometry restraints manager: 1.41 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: 5978 15.26 - 30.51: 636 30.51 - 45.77: 150 45.77 - 61.03: 40 61.03 - 76.28: 6 Dihedral angle restraints: 6810 sinusoidal: 2736 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 6807 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: 0.940 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.260 Find NCS groups from input model: 0.240 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:8.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 : 13.895 76.283 4178 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/Z covalent geometry : bond 0.01001 / 0.45 (11562) covalent geometry : angle 0.94403 / 0.51 (15738) hydrogen bonds : bond 0.15286 / 9.76 ( 588) hydrogen bonds : angle 6.09939 / 4.24 ( 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 : 0.456 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: 0.5160 time to fit residues: 85.1343 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 : 0.430 ------------------------------------------------------------------------------- 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... 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 = 0.3355 r_free = 0.3355 target = 0.113295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.076305 restraints weight = 15338.563| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.20 r_work: 0.2652 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11562 Z= 0.128 Angle : 0.619 16.216 15738 Z= 0.323 Chirality : 0.042 0.156 1876 Planarity : 0.005 0.069 1920 Dihedral : 8.406 97.803 1630 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.07 % Allowed : 9.08 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.31 (0.22), residues: 1398 helix: -0.20 (0.17), residues: 880 sheet: 1.51 (0.82), residues: 36 loop : -2.25 (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 A 9 PHE 0.020 0.001 PHE B 627 TRP 0.011 0.001 TRP A 63 HIS 0.008 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (11562) covalent geometry : angle 0.61905 / 0.32 (15738) hydrogen bonds : bond 0.04520 / 2.95 ( 588) hydrogen bonds : angle 4.22799 / 2.99 ( 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 121 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.549 Fit side-chains REVERT: A 24 ASN cc_start: 0.9097 (m-40) cc_final: 0.8684 (m110) REVERT: A 58 PHE cc_start: 0.7437 (m-80) cc_final: 0.7175 (m-80) REVERT: A 281 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7037 (mmm-85) REVERT: A 606 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8074 (pp20) REVERT: B 24 ASN cc_start: 0.9040 (m-40) cc_final: 0.8558 (m110) REVERT: B 58 PHE cc_start: 0.7535 (m-80) cc_final: 0.7257 (m-80) REVERT: B 99 ASP cc_start: 0.8589 (t0) cc_final: 0.8364 (t0) REVERT: B 281 ARG cc_start: 0.7418 (ttm-80) cc_final: 0.6998 (mmm-85) REVERT: B 529 MET cc_start: 0.9133 (mmm) cc_final: 0.8905 (mmt) outliers start: 13 outliers final: 7 residues processed: 113 average time/residue: 0.4640 time to fit residues: 57.9692 Evaluate side-chains 101 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 606 GLU 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: 6.9990 chunk 64 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 70 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3344 r_free = 0.3344 target = 0.112435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.075446 restraints weight = 15461.254| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.21 r_work: 0.2646 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11562 Z= 0.150 Angle : 0.601 15.942 15738 Z= 0.310 Chirality : 0.043 0.316 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.832 96.602 1626 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.06 % Allowed : 9.08 % Favored : 88.86 % 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: -0.38 (0.23), residues: 1398 helix: 0.55 (0.18), residues: 878 sheet: 1.64 (0.82), residues: 36 loop : -1.88 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.011 0.001 TYR B 9 PHE 0.017 0.001 PHE A 130 TRP 0.012 0.001 TRP A 63 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (11562) covalent geometry : angle 0.60054 / 0.31 (15738) hydrogen bonds : bond 0.04306 / 2.83 ( 588) hydrogen bonds : angle 3.93637 / 2.79 ( 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 127 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.421 Fit side-chains REVERT: A 24 ASN cc_start: 0.9159 (m-40) cc_final: 0.8797 (m110) REVERT: A 58 PHE cc_start: 0.7503 (m-80) cc_final: 0.7224 (m-80) REVERT: A 281 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7112 (mmm-85) REVERT: A 606 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8061 (pp20) REVERT: B 24 ASN cc_start: 0.9094 (m-40) cc_final: 0.8721 (m110) REVERT: B 26 LYS cc_start: 0.8573 (ptmm) cc_final: 0.8342 (ptmt) REVERT: B 58 PHE cc_start: 0.7559 (m-80) cc_final: 0.7287 (m-80) REVERT: B 99 ASP cc_start: 0.8600 (t0) cc_final: 0.8399 (t0) REVERT: B 281 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.7048 (mmm-85) REVERT: B 529 MET cc_start: 0.9130 (mmm) cc_final: 0.8879 (mmt) outliers start: 25 outliers final: 14 residues processed: 117 average time/residue: 0.4267 time to fit residues: 55.4767 Evaluate side-chains 108 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 606 GLU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 71 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.075156 restraints weight = 15569.850| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.21 r_work: 0.2641 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11562 Z= 0.172 Angle : 0.633 16.851 15738 Z= 0.322 Chirality : 0.045 0.381 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.911 113.347 1626 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.73 % Allowed : 10.81 % Favored : 87.46 % 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: -0.15 (0.23), residues: 1398 helix: 0.73 (0.19), residues: 878 sheet: 1.70 (0.82), residues: 36 loop : -1.79 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.012 0.001 TYR B 9 PHE 0.018 0.001 PHE A 130 TRP 0.013 0.001 TRP B 63 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (11562) covalent geometry : angle 0.63251 / 0.32 (15738) hydrogen bonds : bond 0.04249 / 2.78 ( 588) hydrogen bonds : angle 3.90633 / 2.77 ( 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 114 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.433 Fit side-chains REVERT: A 38 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7280 (m-70) REVERT: A 48 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7726 (mp10) REVERT: A 58 PHE cc_start: 0.7469 (m-80) cc_final: 0.7190 (m-80) REVERT: A 281 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.7111 (mmm-85) REVERT: B 24 ASN cc_start: 0.9092 (m-40) cc_final: 0.8684 (m110) REVERT: B 38 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7263 (m-70) REVERT: B 58 PHE cc_start: 0.7506 (m-80) cc_final: 0.7207 (m-80) REVERT: B 99 ASP cc_start: 0.8578 (t0) cc_final: 0.8376 (t0) REVERT: B 281 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7076 (mmm-85) REVERT: B 529 MET cc_start: 0.9109 (mmm) cc_final: 0.8853 (mmt) REVERT: B 698 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8224 (mp0) outliers start: 21 outliers final: 14 residues processed: 105 average time/residue: 0.4525 time to fit residues: 52.1503 Evaluate side-chains 106 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.075187 restraints weight = 15582.183| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.22 r_work: 0.2645 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11562 Z= 0.172 Angle : 0.632 16.851 15738 Z= 0.322 Chirality : 0.045 0.381 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.964 118.116 1626 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.32 % Allowed : 11.47 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.15 (0.23), residues: 1398 helix: 0.73 (0.19), residues: 878 sheet: 1.70 (0.82), residues: 36 loop : -1.79 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.012 0.001 TYR B 9 PHE 0.018 0.001 PHE A 130 TRP 0.013 0.001 TRP B 63 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (11562) covalent geometry : angle 0.63244 / 0.32 (15738) hydrogen bonds : bond 0.04249 / 2.78 ( 588) hydrogen bonds : angle 3.90632 / 2.77 ( 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 106 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.479 Fit side-chains REVERT: A 38 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7274 (m-70) REVERT: A 48 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7726 (mp10) REVERT: A 58 PHE cc_start: 0.7472 (m-80) cc_final: 0.7193 (m-80) REVERT: A 281 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7094 (mmm-85) REVERT: B 24 ASN cc_start: 0.9089 (m-40) cc_final: 0.8682 (m110) REVERT: B 38 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7255 (m-70) REVERT: B 58 PHE cc_start: 0.7514 (m-80) cc_final: 0.7215 (m-80) REVERT: B 99 ASP cc_start: 0.8584 (t0) cc_final: 0.8383 (t0) REVERT: B 281 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.7059 (mmm-85) REVERT: B 529 MET cc_start: 0.9110 (mmm) cc_final: 0.8855 (mmt) outliers start: 16 outliers final: 14 residues processed: 99 average time/residue: 0.4543 time to fit residues: 49.8617 Evaluate side-chains 106 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 684 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3339 r_free = 0.3339 target = 0.112155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.075364 restraints weight = 15544.379| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.17 r_work: 0.2650 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11562 Z= 0.172 Angle : 0.632 16.856 15738 Z= 0.322 Chirality : 0.045 0.380 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.989 118.114 1626 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.32 % Allowed : 11.47 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.15 (0.23), residues: 1398 helix: 0.73 (0.19), residues: 878 sheet: 1.70 (0.82), residues: 36 loop : -1.79 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.012 0.001 TYR B 9 PHE 0.018 0.001 PHE A 130 TRP 0.013 0.001 TRP B 63 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (11562) covalent geometry : angle 0.63207 / 0.32 (15738) hydrogen bonds : bond 0.04251 / 2.79 ( 588) hydrogen bonds : angle 3.90630 / 2.77 ( 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 105 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.366 Fit side-chains REVERT: A 38 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7297 (m-70) REVERT: A 48 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7739 (mp10) REVERT: A 58 PHE cc_start: 0.7523 (m-80) cc_final: 0.7245 (m-80) REVERT: A 281 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7126 (mmm-85) REVERT: B 24 ASN cc_start: 0.9096 (m-40) cc_final: 0.8705 (m110) REVERT: B 38 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7276 (m-70) REVERT: B 58 PHE cc_start: 0.7564 (m-80) cc_final: 0.7268 (m-80) REVERT: B 281 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7091 (mmm-85) REVERT: B 529 MET cc_start: 0.9123 (mmm) cc_final: 0.8870 (mmt) outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 0.4817 time to fit residues: 52.2855 Evaluate side-chains 105 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 684 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 57 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 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: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.075259 restraints weight = 15452.119| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.20 r_work: 0.2647 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11562 Z= 0.172 Angle : 0.629 16.913 15738 Z= 0.320 Chirality : 0.044 0.371 1876 Planarity : 0.004 0.063 1920 Dihedral : 8.012 118.087 1626 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.40 % Allowed : 11.30 % Favored : 87.29 % 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: -0.15 (0.23), residues: 1398 helix: 0.74 (0.19), residues: 878 sheet: 1.70 (0.82), residues: 36 loop : -1.79 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 502 TYR 0.012 0.001 TYR B 9 PHE 0.018 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/Z covalent geometry : bond 0.00408 / 0.17 (11562) covalent geometry : angle 0.62884 / 0.32 (15738) hydrogen bonds : bond 0.04235 / 2.78 ( 588) hydrogen bonds : angle 3.90701 / 2.77 ( 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 106 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.456 Fit side-chains REVERT: A 38 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7290 (m-70) REVERT: A 48 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7745 (mp10) REVERT: A 58 PHE cc_start: 0.7531 (m-80) cc_final: 0.7253 (m-80) REVERT: A 281 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.7129 (mmm-85) REVERT: B 24 ASN cc_start: 0.9101 (m-40) cc_final: 0.8711 (m110) REVERT: B 38 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7269 (m-70) REVERT: B 58 PHE cc_start: 0.7575 (m-80) cc_final: 0.7308 (m-80) REVERT: B 281 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.7094 (mmm-85) REVERT: B 529 MET cc_start: 0.9127 (mmm) cc_final: 0.8872 (mmt) outliers start: 17 outliers final: 16 residues processed: 100 average time/residue: 0.4564 time to fit residues: 50.6155 Evaluate side-chains 107 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 558 ASP 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 558 ASP 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: 2.9990 chunk 123 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.074982 restraints weight = 15497.122| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.20 r_work: 0.2638 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: 0.8672 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11562 Z= 0.174 Angle : 0.633 17.319 15738 Z= 0.325 Chirality : 0.044 0.149 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.845 107.697 1626 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.40 % Allowed : 11.22 % Favored : 87.38 % 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: 0.90 (0.19), residues: 874 sheet: 1.80 (0.81), residues: 36 loop : -1.73 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 281 TYR 0.012 0.001 TYR B 9 PHE 0.018 0.001 PHE A 130 TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (11562) covalent geometry : angle 0.63258 / 0.32 (15738) hydrogen bonds : bond 0.04277 / 2.80 ( 588) hydrogen bonds : angle 3.88222 / 2.75 ( 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 112 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.458 Fit side-chains REVERT: A 38 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7277 (m-70) REVERT: A 48 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7709 (mp10) REVERT: A 58 PHE cc_start: 0.7449 (m-80) cc_final: 0.7168 (m-80) REVERT: A 259 ILE cc_start: 0.8617 (pp) cc_final: 0.8233 (mp) REVERT: B 24 ASN cc_start: 0.9088 (m-40) cc_final: 0.8701 (m110) REVERT: B 26 LYS cc_start: 0.8598 (ptmm) cc_final: 0.8235 (pmmt) REVERT: B 38 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7330 (m-70) REVERT: B 58 PHE cc_start: 0.7501 (m-80) cc_final: 0.7225 (m-80) REVERT: B 281 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7110 (mmm-85) REVERT: B 293 GLU cc_start: 0.6950 (mp0) cc_final: 0.6724 (mp0) outliers start: 17 outliers final: 14 residues processed: 105 average time/residue: 0.4078 time to fit residues: 47.6770 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 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: 0.0000 chunk 127 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 0.1980 chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 113 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3335 r_free = 0.3335 target = 0.111900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.075122 restraints weight = 15349.070| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.16 r_work: 0.2643 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11562 Z= 0.174 Angle : 0.633 17.320 15738 Z= 0.325 Chirality : 0.044 0.149 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.942 118.116 1626 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.32 % Allowed : 11.55 % Favored : 87.13 % 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: 0.90 (0.19), residues: 874 sheet: 1.80 (0.81), residues: 36 loop : -1.73 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 281 TYR 0.012 0.001 TYR B 9 PHE 0.018 0.001 PHE A 130 TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (11562) covalent geometry : angle 0.63250 / 0.32 (15738) hydrogen bonds : bond 0.04277 / 2.80 ( 588) hydrogen bonds : angle 3.88222 / 2.75 ( 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: 16 poor density : 93 time to evaluate : 0.456 Fit side-chains REVERT: A 38 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7300 (m-70) REVERT: A 48 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7723 (mp10) REVERT: A 58 PHE cc_start: 0.7496 (m-80) cc_final: 0.7216 (m-80) REVERT: A 259 ILE cc_start: 0.8666 (pp) cc_final: 0.8281 (mp) REVERT: B 24 ASN cc_start: 0.9097 (m-40) cc_final: 0.8726 (m110) REVERT: B 26 LYS cc_start: 0.8607 (ptmm) cc_final: 0.8281 (pmmt) REVERT: B 38 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7351 (m-70) REVERT: B 58 PHE cc_start: 0.7553 (m-80) cc_final: 0.7281 (m-80) REVERT: B 281 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7135 (mmm-85) REVERT: B 293 GLU cc_start: 0.6992 (mp0) cc_final: 0.6760 (mp0) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.4400 time to fit residues: 49.3039 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 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 369 LEU 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 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: 3.9990 chunk 6 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3335 r_free = 0.3335 target = 0.111901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.074905 restraints weight = 15457.989| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.21 r_work: 0.2637 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11562 Z= 0.174 Angle : 0.631 17.338 15738 Z= 0.324 Chirality : 0.044 0.146 1876 Planarity : 0.004 0.063 1920 Dihedral : 7.960 118.113 1626 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.24 % Allowed : 11.63 % Favored : 87.13 % 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: 0.90 (0.19), residues: 874 sheet: 1.80 (0.81), residues: 36 loop : -1.73 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.012 0.001 TYR B 9 PHE 0.018 0.001 PHE A 130 TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (11562) covalent geometry : angle 0.63136 / 0.32 (15738) hydrogen bonds : bond 0.04277 / 2.80 ( 588) hydrogen bonds : angle 3.88210 / 2.75 ( 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 108 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.424 Fit side-chains REVERT: A 38 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.7282 (m-70) REVERT: A 48 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7710 (mp10) REVERT: A 58 PHE cc_start: 0.7449 (m-80) cc_final: 0.7168 (m-80) REVERT: A 259 ILE cc_start: 0.8609 (pp) cc_final: 0.8235 (mp) REVERT: B 24 ASN cc_start: 0.9090 (m-40) cc_final: 0.8704 (m110) REVERT: B 26 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8234 (pmmt) REVERT: B 38 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7336 (m-70) REVERT: B 58 PHE cc_start: 0.7502 (m-80) cc_final: 0.7228 (m-80) REVERT: B 281 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7110 (mmm-85) REVERT: B 293 GLU cc_start: 0.6953 (mp0) cc_final: 0.6729 (mp0) outliers start: 15 outliers final: 14 residues processed: 101 average time/residue: 0.4400 time to fit residues: 49.2939 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 79 optimal weight: 0.0870 chunk 115 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3335 r_free = 0.3335 target = 0.111920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.074917 restraints weight = 15465.696| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.21 r_work: 0.2637 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11562 Z= 0.172 Angle : 0.629 17.377 15738 Z= 0.322 Chirality : 0.044 0.140 1876 Planarity : 0.004 0.062 1920 Dihedral : 8.027 118.106 1626 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.24 % Allowed : 11.63 % Favored : 87.13 % 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: 0.90 (0.19), residues: 874 sheet: 1.80 (0.81), residues: 36 loop : -1.72 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 281 TYR 0.012 0.001 TYR B 9 PHE 0.018 0.001 PHE A 130 TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS A 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (11562) covalent geometry : angle 0.62911 / 0.32 (15738) hydrogen bonds : bond 0.04263 / 2.79 ( 588) hydrogen bonds : angle 3.88226 / 2.75 ( 1716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.53 seconds wall clock time: 59 minutes 45.05 seconds (3585.05 seconds total)