Starting phenix.real_space_refine on Sun Dec 29 20:43:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xuj_33471/12_2024/7xuj_33471.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xuj_33471/12_2024/7xuj_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_33471/12_2024/7xuj_33471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xuj_33471/12_2024/7xuj_33471.map" model { file = "/net/cci-nas-00/data/ceres_data/7xuj_33471/12_2024/7xuj_33471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xuj_33471/12_2024/7xuj_33471.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.15, per 1000 atoms: 0.63 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: 2.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.03 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: 3.47 Time building geometry restraints manager: 3.07 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: 0.00 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.740 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- 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= 0.642 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.002 TRP B 63 HIS 0.007 0.001 HIS A 38 PHE 0.027 0.002 PHE A 130 TYR 0.026 0.002 TYR B 9 ARG 0.004 0.001 ARG A 399 *********************** 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 : 1.376 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: 1.0812 time to fit residues: 179.1802 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 : 1.298 ------------------------------------------------------------------------------- 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 118 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11562 Z= 0.190 Angle : 0.610 15.794 15738 Z= 0.317 Chirality : 0.042 0.151 1876 Planarity : 0.005 0.067 1920 Dihedral : 8.133 94.829 2094 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.16 % Allowed : 8.91 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1398 helix: -0.11 (0.17), residues: 882 sheet: 1.56 (0.82), residues: 36 loop : -2.18 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.008 0.001 HIS B 31 PHE 0.021 0.001 PHE B 627 TYR 0.009 0.001 TYR B 107 ARG 0.007 0.000 ARG A 312 *********************** 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: 14 poor density : 107 time to evaluate : 1.308 Fit side-chains REVERT: A 58 PHE cc_start: 0.7237 (m-80) cc_final: 0.6953 (m-80) REVERT: A 99 ASP cc_start: 0.7834 (t0) cc_final: 0.7633 (t0) REVERT: A 281 ARG cc_start: 0.7483 (ttm-80) cc_final: 0.7100 (mmm-85) REVERT: B 24 ASN cc_start: 0.8828 (m-40) cc_final: 0.8539 (m110) REVERT: B 58 PHE cc_start: 0.7324 (m-80) cc_final: 0.7067 (m-80) REVERT: B 99 ASP cc_start: 0.7957 (t0) cc_final: 0.7735 (t0) REVERT: B 281 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.7091 (mmm-85) outliers start: 14 outliers final: 7 residues processed: 112 average time/residue: 1.0677 time to fit residues: 132.0416 Evaluate side-chains 100 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.164 Angle : 0.590 15.201 15738 Z= 0.305 Chirality : 0.042 0.148 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.342 59.566 2090 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1398 helix: 0.61 (0.18), residues: 870 sheet: 1.66 (0.83), residues: 36 loop : -2.03 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.018 0.002 HIS A 31 PHE 0.018 0.001 PHE A 130 TYR 0.008 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 *********************** 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 : 1.222 Fit side-chains REVERT: A 38 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7377 (m-70) REVERT: A 58 PHE cc_start: 0.7212 (m-80) cc_final: 0.6905 (m-80) REVERT: A 99 ASP cc_start: 0.7812 (t0) cc_final: 0.7608 (t0) REVERT: A 281 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7092 (mmm-85) REVERT: B 24 ASN cc_start: 0.8834 (m-40) cc_final: 0.8515 (m110) REVERT: B 38 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7362 (m-70) REVERT: B 58 PHE cc_start: 0.7267 (m-80) cc_final: 0.6985 (m-80) REVERT: B 99 ASP cc_start: 0.7924 (t0) cc_final: 0.7701 (t0) REVERT: B 281 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7140 (mmm-85) outliers start: 24 outliers final: 12 residues processed: 116 average time/residue: 1.0431 time to fit residues: 134.0404 Evaluate side-chains 108 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 171 ASP Chi-restraints excluded: chain A residue 238 THR 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 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 125 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.164 Angle : 0.590 15.201 15738 Z= 0.305 Chirality : 0.042 0.148 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.767 118.116 2090 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.16 % Allowed : 11.06 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1398 helix: 0.61 (0.18), residues: 870 sheet: 1.66 (0.83), residues: 36 loop : -2.03 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.018 0.002 HIS A 31 PHE 0.018 0.001 PHE A 130 TYR 0.008 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 *********************** 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 108 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.339 Fit side-chains REVERT: A 38 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7377 (m-70) REVERT: A 58 PHE cc_start: 0.7212 (m-80) cc_final: 0.6905 (m-80) REVERT: A 99 ASP cc_start: 0.7813 (t0) cc_final: 0.7608 (t0) REVERT: A 281 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7092 (mmm-85) REVERT: B 24 ASN cc_start: 0.8835 (m-40) cc_final: 0.8515 (m110) REVERT: B 38 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7362 (m-70) REVERT: B 58 PHE cc_start: 0.7267 (m-80) cc_final: 0.6985 (m-80) REVERT: B 99 ASP cc_start: 0.7923 (t0) cc_final: 0.7701 (t0) REVERT: B 281 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7140 (mmm-85) outliers start: 14 outliers final: 12 residues processed: 100 average time/residue: 1.1764 time to fit residues: 128.8520 Evaluate side-chains 104 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 171 ASP Chi-restraints excluded: chain A residue 238 THR 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 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 76 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.164 Angle : 0.590 15.201 15738 Z= 0.305 Chirality : 0.042 0.148 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.767 118.116 2090 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.16 % Allowed : 11.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1398 helix: 0.61 (0.18), residues: 870 sheet: 1.66 (0.83), residues: 36 loop : -2.03 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.018 0.002 HIS A 31 PHE 0.018 0.001 PHE A 130 TYR 0.008 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 *********************** 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 104 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.287 Fit side-chains REVERT: A 38 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7377 (m-70) REVERT: A 58 PHE cc_start: 0.7212 (m-80) cc_final: 0.6905 (m-80) REVERT: A 99 ASP cc_start: 0.7813 (t0) cc_final: 0.7609 (t0) REVERT: A 281 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7092 (mmm-85) REVERT: B 24 ASN cc_start: 0.8835 (m-40) cc_final: 0.8515 (m110) REVERT: B 38 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7362 (m-70) REVERT: B 58 PHE cc_start: 0.7267 (m-80) cc_final: 0.6985 (m-80) REVERT: B 99 ASP cc_start: 0.7924 (t0) cc_final: 0.7701 (t0) REVERT: B 281 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7140 (mmm-85) outliers start: 14 outliers final: 12 residues processed: 96 average time/residue: 1.1639 time to fit residues: 123.0935 Evaluate side-chains 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 171 ASP Chi-restraints excluded: chain A residue 238 THR 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 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 121 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.164 Angle : 0.590 15.201 15738 Z= 0.305 Chirality : 0.042 0.148 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.767 118.116 2090 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.16 % Allowed : 11.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1398 helix: 0.61 (0.18), residues: 870 sheet: 1.66 (0.83), residues: 36 loop : -2.03 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.018 0.002 HIS A 31 PHE 0.018 0.001 PHE A 130 TYR 0.008 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 *********************** 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 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.315 Fit side-chains REVERT: A 38 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7377 (m-70) REVERT: A 58 PHE cc_start: 0.7212 (m-80) cc_final: 0.6905 (m-80) REVERT: A 99 ASP cc_start: 0.7813 (t0) cc_final: 0.7609 (t0) REVERT: A 281 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7092 (mmm-85) REVERT: B 24 ASN cc_start: 0.8835 (m-40) cc_final: 0.8515 (m110) REVERT: B 38 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7362 (m-70) REVERT: B 58 PHE cc_start: 0.7267 (m-80) cc_final: 0.6985 (m-80) REVERT: B 99 ASP cc_start: 0.7923 (t0) cc_final: 0.7701 (t0) REVERT: B 281 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7140 (mmm-85) outliers start: 14 outliers final: 12 residues processed: 95 average time/residue: 1.1227 time to fit residues: 117.6633 Evaluate side-chains 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 171 ASP Chi-restraints excluded: chain A residue 238 THR 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 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 15 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 0.0020 chunk 83 optimal weight: 0.7980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.164 Angle : 0.590 15.201 15738 Z= 0.305 Chirality : 0.042 0.148 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.767 118.116 2090 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.16 % Allowed : 11.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1398 helix: 0.61 (0.18), residues: 870 sheet: 1.66 (0.83), residues: 36 loop : -2.03 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.018 0.002 HIS A 31 PHE 0.018 0.001 PHE A 130 TYR 0.008 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 *********************** 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 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.290 Fit side-chains REVERT: A 38 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7377 (m-70) REVERT: A 58 PHE cc_start: 0.7212 (m-80) cc_final: 0.6905 (m-80) REVERT: A 99 ASP cc_start: 0.7813 (t0) cc_final: 0.7609 (t0) REVERT: A 281 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7092 (mmm-85) REVERT: B 24 ASN cc_start: 0.8835 (m-40) cc_final: 0.8515 (m110) REVERT: B 38 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7362 (m-70) REVERT: B 58 PHE cc_start: 0.7267 (m-80) cc_final: 0.6985 (m-80) REVERT: B 99 ASP cc_start: 0.7923 (t0) cc_final: 0.7701 (t0) REVERT: B 281 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7140 (mmm-85) outliers start: 14 outliers final: 12 residues processed: 95 average time/residue: 1.0993 time to fit residues: 115.4667 Evaluate side-chains 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 171 ASP Chi-restraints excluded: chain A residue 238 THR 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 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 53 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.164 Angle : 0.590 15.201 15738 Z= 0.305 Chirality : 0.042 0.148 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.767 118.116 2090 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.16 % Allowed : 11.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1398 helix: 0.61 (0.18), residues: 870 sheet: 1.66 (0.83), residues: 36 loop : -2.03 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.018 0.002 HIS A 31 PHE 0.018 0.001 PHE A 130 TYR 0.008 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 *********************** 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 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.265 Fit side-chains REVERT: A 38 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7377 (m-70) REVERT: A 58 PHE cc_start: 0.7212 (m-80) cc_final: 0.6905 (m-80) REVERT: A 99 ASP cc_start: 0.7813 (t0) cc_final: 0.7609 (t0) REVERT: A 281 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7092 (mmm-85) REVERT: B 24 ASN cc_start: 0.8835 (m-40) cc_final: 0.8515 (m110) REVERT: B 38 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7362 (m-70) REVERT: B 58 PHE cc_start: 0.7267 (m-80) cc_final: 0.6985 (m-80) REVERT: B 99 ASP cc_start: 0.7923 (t0) cc_final: 0.7701 (t0) REVERT: B 281 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7140 (mmm-85) outliers start: 14 outliers final: 12 residues processed: 95 average time/residue: 1.0891 time to fit residues: 114.0262 Evaluate side-chains 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 171 ASP Chi-restraints excluded: chain A residue 238 THR 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 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 117 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 129 optimal weight: 0.0470 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.164 Angle : 0.590 15.201 15738 Z= 0.305 Chirality : 0.042 0.148 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.767 118.116 2090 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.16 % Allowed : 11.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1398 helix: 0.61 (0.18), residues: 870 sheet: 1.66 (0.83), residues: 36 loop : -2.03 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.018 0.002 HIS A 31 PHE 0.018 0.001 PHE A 130 TYR 0.008 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 *********************** 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 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.386 Fit side-chains REVERT: A 38 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7377 (m-70) REVERT: A 58 PHE cc_start: 0.7212 (m-80) cc_final: 0.6905 (m-80) REVERT: A 99 ASP cc_start: 0.7813 (t0) cc_final: 0.7609 (t0) REVERT: A 281 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7092 (mmm-85) REVERT: B 24 ASN cc_start: 0.8835 (m-40) cc_final: 0.8515 (m110) REVERT: B 38 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7362 (m-70) REVERT: B 58 PHE cc_start: 0.7267 (m-80) cc_final: 0.6985 (m-80) REVERT: B 99 ASP cc_start: 0.7923 (t0) cc_final: 0.7701 (t0) REVERT: B 281 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7140 (mmm-85) outliers start: 14 outliers final: 12 residues processed: 95 average time/residue: 1.1315 time to fit residues: 119.1641 Evaluate side-chains 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 171 ASP Chi-restraints excluded: chain A residue 238 THR 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 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 81 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 128 optimal weight: 0.0000 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.164 Angle : 0.590 15.201 15738 Z= 0.305 Chirality : 0.042 0.148 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.767 118.116 2090 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.16 % Allowed : 11.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1398 helix: 0.61 (0.18), residues: 870 sheet: 1.66 (0.83), residues: 36 loop : -2.03 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.018 0.002 HIS A 31 PHE 0.018 0.001 PHE A 130 TYR 0.008 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 ********************** 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 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.429 Fit side-chains REVERT: A 38 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7377 (m-70) REVERT: A 58 PHE cc_start: 0.7212 (m-80) cc_final: 0.6905 (m-80) REVERT: A 99 ASP cc_start: 0.7813 (t0) cc_final: 0.7609 (t0) REVERT: A 281 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7092 (mmm-85) REVERT: B 24 ASN cc_start: 0.8835 (m-40) cc_final: 0.8515 (m110) REVERT: B 38 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7362 (m-70) REVERT: B 58 PHE cc_start: 0.7267 (m-80) cc_final: 0.6985 (m-80) REVERT: B 99 ASP cc_start: 0.7923 (t0) cc_final: 0.7701 (t0) REVERT: B 281 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7140 (mmm-85) outliers start: 14 outliers final: 12 residues processed: 95 average time/residue: 1.1337 time to fit residues: 118.5701 Evaluate side-chains 103 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 171 ASP Chi-restraints excluded: chain A residue 238 THR 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 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 34 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 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 = 0.3361 r_free = 0.3361 target = 0.113625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.076938 restraints weight = 15290.562| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.20 r_work: 0.2673 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11562 Z= 0.164 Angle : 0.590 15.201 15738 Z= 0.305 Chirality : 0.042 0.148 1876 Planarity : 0.004 0.064 1920 Dihedral : 7.767 118.116 2090 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.16 % Allowed : 11.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1398 helix: 0.61 (0.18), residues: 870 sheet: 1.66 (0.83), residues: 36 loop : -2.03 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.018 0.002 HIS A 31 PHE 0.018 0.001 PHE A 130 TYR 0.008 0.001 TYR B 9 ARG 0.005 0.000 ARG A 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.26 seconds wall clock time: 55 minutes 56.67 seconds (3356.67 seconds total)