Starting phenix.real_space_refine on Thu Jul 2 17:02:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qo9_14087/07_2026/7qo9_14087.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qo9_14087/07_2026/7qo9_14087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qo9_14087/07_2026/7qo9_14087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qo9_14087/07_2026/7qo9_14087.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7qo9_14087/07_2026/7qo9_14087.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qo9_14087/07_2026/7qo9_14087.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qo9_14087/07_2026/7qo9_14087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qo9_14087/07_2026/7qo9_14087.map" } resolution = 3.88 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= 0.012 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 45 5.16 5 C 5830 2.51 5 N 1523 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 9180 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4568 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 562} Chain breaks: 14 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4486 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 26, 'TRANS': 551} Chain breaks: 6 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.00, per 1000 atoms: 0.22 Number of scatterers: 9180 At special positions: 0 Unit cell: (87.5022, 112.046, 122.717, 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 45 16.00 O 1782 8.00 N 1523 7.00 C 5830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 231 " " NAG A1302 " - " ASN A 279 " " NAG C 1 " - " ASN A 160 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 135 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 273.3 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 17 sheets defined 26.2% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.661A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.500A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 Processing helix chain 'A' and resid 846 through 852 removed outlier: 3.589A pdb=" N PHE A 852 " --> pdb=" O CYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 874 Processing helix chain 'A' and resid 943 through 962 removed outlier: 4.873A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1022 removed outlier: 4.599A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.769A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 removed outlier: 3.762A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 757 through 779 removed outlier: 3.565A pdb=" N ILE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 825 through 827 No H-bonds generated for 'chain 'B' and resid 825 through 827' Processing helix chain 'B' and resid 863 through 864 No H-bonds generated for 'chain 'B' and resid 863 through 864' Processing helix chain 'B' and resid 866 through 868 No H-bonds generated for 'chain 'B' and resid 866 through 868' Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.739A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 980 Processing helix chain 'B' and resid 982 through 1022 removed outlier: 4.466A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.205A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.508A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA6, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.861A pdb=" N SER A 114 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 126 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE A 163 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL A 128 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS A 161 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER A 157 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.626A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 651 through 657 removed outlier: 6.058A pdb=" N THR A 693 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN A 655 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 724 through 725 Processing sheet with id=AB1, first strand: chain 'A' and resid 732 through 733 Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 316 removed outlier: 3.807A pdb=" N THR B 312 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.500A pdb=" N ASN B 539 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 352 through 355 removed outlier: 3.836A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.547A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.708A pdb=" N ARG B 506 " --> pdb=" O TRP B 433 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.593A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 732 through 733 300 hydrogen bonds defined for protein. 819 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: 1.16 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1899 1.33 - 1.45: 2235 1.45 - 1.58: 5160 1.58 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 9349 Sorted by residual: bond pdb=" N GLN A 625 " pdb=" CA GLN A 625 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.31e+01 bond pdb=" CA SER B 491 " pdb=" CB SER B 491 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.39e-02 5.18e+03 1.30e+01 bond pdb=" N VAL B 480 " pdb=" CA VAL B 480 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N ASP A 624 " pdb=" CA ASP A 624 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.20e-02 6.94e+03 9.24e+00 bond pdb=" N CYS B 485 " pdb=" CA CYS B 485 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.26e-02 6.30e+03 7.82e+00 ... (remaining 9344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 12443 2.37 - 4.74: 203 4.74 - 7.10: 37 7.10 - 9.47: 3 9.47 - 11.84: 4 Bond angle restraints: 12690 Sorted by residual: angle pdb=" N PRO A 628 " pdb=" CA PRO A 628 " pdb=" CB PRO A 628 " ideal model delta sigma weight residual 103.25 92.75 10.50 1.05e+00 9.07e-01 1.00e+02 angle pdb=" C TYR B 448 " pdb=" CA TYR B 448 " pdb=" CB TYR B 448 " ideal model delta sigma weight residual 110.88 99.97 10.91 1.57e+00 4.06e-01 4.83e+01 angle pdb=" C TYR B 486 " pdb=" CA TYR B 486 " pdb=" CB TYR B 486 " ideal model delta sigma weight residual 109.83 97.99 11.84 1.75e+00 3.27e-01 4.58e+01 angle pdb=" C TYR B 446 " pdb=" CA TYR B 446 " pdb=" CB TYR B 446 " ideal model delta sigma weight residual 114.87 104.90 9.97 1.51e+00 4.39e-01 4.36e+01 angle pdb=" CA ASP A 624 " pdb=" C ASP A 624 " pdb=" O ASP A 624 " ideal model delta sigma weight residual 121.31 116.01 5.30 1.07e+00 8.73e-01 2.45e+01 ... (remaining 12685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 4937 17.02 - 34.05: 471 34.05 - 51.07: 96 51.07 - 68.09: 24 68.09 - 85.11: 14 Dihedral angle restraints: 5542 sinusoidal: 2159 harmonic: 3383 Sorted by residual: dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual -86.00 -167.55 81.55 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS B 535 " pdb=" SG CYS B 535 " pdb=" SG CYS B 587 " pdb=" CB CYS B 587 " ideal model delta sinusoidal sigma weight residual -86.00 -5.51 -80.49 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 -11.72 -74.28 1 1.00e+01 1.00e-02 7.00e+01 ... (remaining 5539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1436 0.110 - 0.219: 48 0.219 - 0.329: 8 0.329 - 0.438: 3 0.438 - 0.548: 3 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA TYR B 448 " pdb=" N TYR B 448 " pdb=" C TYR B 448 " pdb=" CB TYR B 448 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 160 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CA TYR B 446 " pdb=" N TYR B 446 " pdb=" C TYR B 446 " pdb=" CB TYR B 446 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 4.96e+00 ... (remaining 1495 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 627 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C THR A 627 " -0.055 2.00e-02 2.50e+03 pdb=" O THR A 627 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO A 628 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 226 " 0.043 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO A 227 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 79 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 80 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " 0.035 5.00e-02 4.00e+02 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 528 2.72 - 3.27: 9666 3.27 - 3.81: 14147 3.81 - 4.36: 16230 4.36 - 4.90: 27275 Nonbonded interactions: 67846 Sorted by model distance: nonbonded pdb=" OH TYR A 89 " pdb=" OE1 GLU A 186 " model vdw 2.179 3.040 nonbonded pdb=" O THR B 863 " pdb=" N MET B 866 " model vdw 2.201 3.120 nonbonded pdb=" O VAL A 619 " pdb=" ND1 HIS A 622 " model vdw 2.232 3.120 nonbonded pdb=" OG SER A 110 " pdb=" OE1 GLN A 132 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 755 " pdb=" OG1 THR A 758 " model vdw 2.251 3.040 ... (remaining 67841 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 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.630 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9375 Z= 0.228 Angle : 0.777 11.839 12751 Z= 0.439 Chirality : 0.056 0.548 1498 Planarity : 0.005 0.066 1615 Dihedral : 14.425 85.114 3303 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.16 % Favored : 90.30 % Rotamer: Outliers : 1.29 % Allowed : 0.50 % Favored : 98.22 % Cbeta Deviations : 0.55 % 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: -1.18 (0.25), residues: 1124 helix: 1.37 (0.33), residues: 272 sheet: -0.07 (0.39), residues: 181 loop : -2.05 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1016 TYR 0.031 0.001 TYR B 450 PHE 0.037 0.001 PHE B 371 TRP 0.007 0.001 TRP B 433 HIS 0.004 0.001 HIS B 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.23 ( 9349) covalent geometry : angle 0.75746 / 0.43 (12690) SS BOND : bond 0.00372 / 0.27 ( 17) SS BOND : angle 1.90374 / 1.06 ( 34) hydrogen bonds : bond 0.14730 / 9.43 ( 300) hydrogen bonds : angle 6.02204 / 4.15 ( 819) link_BETA1-4 : bond 0.00785 / 0.39 ( 4) link_BETA1-4 : angle 3.93467 / 2.07 ( 12) link_NAG-ASN : bond 0.00720 / 0.28 ( 5) link_NAG-ASN : angle 2.69980 / 1.53 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.246 Fit side-chains REVERT: A 290 LEU cc_start: 0.8808 (tt) cc_final: 0.8282 (tt) REVERT: A 773 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8279 (tptt) REVERT: A 774 ASN cc_start: 0.8574 (m110) cc_final: 0.8373 (m110) REVERT: B 446 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6469 (t80) REVERT: B 490 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7177 (tpm170) REVERT: B 770 GLU cc_start: 0.6475 (tm-30) cc_final: 0.6273 (tm-30) REVERT: B 999 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7872 (tm-30) outliers start: 13 outliers final: 4 residues processed: 120 average time/residue: 0.0787 time to fit residues: 13.7636 Evaluate side-chains 77 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 PRO Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 491 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.0370 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 1.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 ASN B 962 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.116340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091039 restraints weight = 28407.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090576 restraints weight = 19353.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.091218 restraints weight = 15721.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.091835 restraints weight = 13333.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.091950 restraints weight = 11834.491| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9375 Z= 0.189 Angle : 0.696 10.811 12751 Z= 0.354 Chirality : 0.047 0.314 1498 Planarity : 0.005 0.069 1615 Dihedral : 5.459 56.197 1247 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.23 % Favored : 89.59 % Rotamer: Outliers : 1.49 % Allowed : 9.12 % Favored : 89.40 % 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: -1.39 (0.24), residues: 1124 helix: 1.43 (0.32), residues: 263 sheet: -0.07 (0.39), residues: 172 loop : -2.26 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 405 TYR 0.015 0.001 TYR B 348 PHE 0.021 0.002 PHE B 371 TRP 0.018 0.002 TRP A 630 HIS 0.004 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 9349) covalent geometry : angle 0.68062 / 0.35 (12690) SS BOND : bond 0.00434 / 0.30 ( 17) SS BOND : angle 1.69888 / 1.00 ( 34) hydrogen bonds : bond 0.04624 / 3.13 ( 300) hydrogen bonds : angle 5.41682 / 3.76 ( 819) link_BETA1-4 : bond 0.00837 / 0.41 ( 4) link_BETA1-4 : angle 3.18192 / 1.69 ( 12) link_NAG-ASN : bond 0.00349 / 0.14 ( 5) link_NAG-ASN : angle 2.20476 / 1.23 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.380 Fit side-chains REVERT: A 290 LEU cc_start: 0.8751 (tt) cc_final: 0.8467 (tt) REVERT: A 291 ASP cc_start: 0.8242 (m-30) cc_final: 0.7828 (m-30) REVERT: A 296 THR cc_start: 0.9131 (m) cc_final: 0.8822 (p) REVERT: A 629 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8063 (t) REVERT: A 833 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7911 (tp-100) REVERT: B 446 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.6676 (t80) REVERT: B 490 ARG cc_start: 0.8128 (mtt90) cc_final: 0.6916 (tpm170) REVERT: B 737 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7763 (tpp) REVERT: B 770 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6537 (tm-30) REVERT: B 999 GLN cc_start: 0.8593 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 1009 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8962 (mt) outliers start: 15 outliers final: 6 residues processed: 91 average time/residue: 0.0810 time to fit residues: 10.6836 Evaluate side-chains 80 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 91 optimal weight: 0.0970 chunk 114 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.117547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.091897 restraints weight = 28322.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092496 restraints weight = 17532.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.093114 restraints weight = 14220.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.093557 restraints weight = 11791.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093687 restraints weight = 10975.644| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9375 Z= 0.129 Angle : 0.635 9.368 12751 Z= 0.320 Chirality : 0.046 0.324 1498 Planarity : 0.004 0.062 1615 Dihedral : 4.983 50.173 1241 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.79 % Favored : 90.04 % Rotamer: Outliers : 1.39 % Allowed : 12.69 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.25 (0.25), residues: 1124 helix: 1.53 (0.32), residues: 269 sheet: 0.03 (0.41), residues: 165 loop : -2.18 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 405 TYR 0.011 0.001 TYR B 348 PHE 0.014 0.001 PHE B 371 TRP 0.007 0.001 TRP A 630 HIS 0.003 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9349) covalent geometry : angle 0.62148 / 0.32 (12690) SS BOND : bond 0.00278 / 0.18 ( 17) SS BOND : angle 1.41546 / 0.84 ( 34) hydrogen bonds : bond 0.04219 / 2.88 ( 300) hydrogen bonds : angle 5.06342 / 3.51 ( 819) link_BETA1-4 : bond 0.00764 / 0.38 ( 4) link_BETA1-4 : angle 3.03777 / 1.61 ( 12) link_NAG-ASN : bond 0.00265 / 0.12 ( 5) link_NAG-ASN : angle 2.07810 / 1.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 629 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8163 (t) REVERT: A 833 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7802 (tp-100) REVERT: B 446 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6639 (t80) REVERT: B 490 ARG cc_start: 0.7973 (mtt90) cc_final: 0.6801 (tpm170) REVERT: B 770 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6458 (tm-30) REVERT: B 999 GLN cc_start: 0.8572 (tm-30) cc_final: 0.7924 (tm-30) outliers start: 14 outliers final: 8 residues processed: 90 average time/residue: 0.0734 time to fit residues: 10.0543 Evaluate side-chains 74 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.115457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090254 restraints weight = 28402.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.090107 restraints weight = 18807.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.090696 restraints weight = 15114.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.091255 restraints weight = 12853.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091440 restraints weight = 11229.539| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9375 Z= 0.180 Angle : 0.662 9.312 12751 Z= 0.335 Chirality : 0.046 0.330 1498 Planarity : 0.005 0.066 1615 Dihedral : 5.034 45.796 1241 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.94 % Favored : 88.88 % Rotamer: Outliers : 1.98 % Allowed : 15.86 % Favored : 82.16 % 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: -1.35 (0.24), residues: 1124 helix: 1.59 (0.32), residues: 263 sheet: 0.24 (0.41), residues: 151 loop : -2.31 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 762 TYR 0.012 0.001 TYR B 348 PHE 0.019 0.001 PHE B 556 TRP 0.008 0.001 TRP A 630 HIS 0.004 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 9349) covalent geometry : angle 0.64816 / 0.33 (12690) SS BOND : bond 0.00373 / 0.24 ( 17) SS BOND : angle 1.51166 / 0.93 ( 34) hydrogen bonds : bond 0.04298 / 2.94 ( 300) hydrogen bonds : angle 5.10550 / 3.55 ( 819) link_BETA1-4 : bond 0.00776 / 0.37 ( 4) link_BETA1-4 : angle 2.99345 / 1.59 ( 12) link_NAG-ASN : bond 0.00241 / 0.10 ( 5) link_NAG-ASN : angle 2.15686 / 1.20 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 833 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7821 (tp-100) REVERT: A 987 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8793 (tm-30) REVERT: B 446 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6698 (t80) REVERT: B 490 ARG cc_start: 0.7980 (mtt90) cc_final: 0.6919 (tpm170) REVERT: B 770 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6807 (tp30) REVERT: B 999 GLN cc_start: 0.8610 (tm-30) cc_final: 0.7973 (tm-30) outliers start: 20 outliers final: 14 residues processed: 88 average time/residue: 0.0869 time to fit residues: 11.0701 Evaluate side-chains 80 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.117296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092155 restraints weight = 28402.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091678 restraints weight = 19289.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092372 restraints weight = 15432.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.092929 restraints weight = 13135.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093067 restraints weight = 11577.324| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9375 Z= 0.118 Angle : 0.629 10.192 12751 Z= 0.314 Chirality : 0.045 0.334 1498 Planarity : 0.004 0.054 1615 Dihedral : 4.789 39.098 1241 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.52 % Favored : 90.39 % Rotamer: Outliers : 1.98 % Allowed : 18.04 % Favored : 79.98 % 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: -1.20 (0.25), residues: 1124 helix: 1.72 (0.33), residues: 263 sheet: 0.31 (0.44), residues: 141 loop : -2.18 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 762 TYR 0.010 0.001 TYR B 492 PHE 0.010 0.001 PHE B 371 TRP 0.006 0.001 TRP A 630 HIS 0.003 0.001 HIS B 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9349) covalent geometry : angle 0.61712 / 0.31 (12690) SS BOND : bond 0.00237 / 0.16 ( 17) SS BOND : angle 1.21766 / 0.75 ( 34) hydrogen bonds : bond 0.03933 / 2.70 ( 300) hydrogen bonds : angle 4.81909 / 3.35 ( 819) link_BETA1-4 : bond 0.00802 / 0.40 ( 4) link_BETA1-4 : angle 2.90945 / 1.54 ( 12) link_NAG-ASN : bond 0.00252 / 0.12 ( 5) link_NAG-ASN : angle 2.07526 / 1.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 773 LYS cc_start: 0.9203 (tptt) cc_final: 0.8336 (tptt) REVERT: A 833 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7702 (tp-100) REVERT: A 987 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8794 (tm-30) REVERT: B 415 ILE cc_start: 0.8379 (mp) cc_final: 0.7854 (tp) REVERT: B 446 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6729 (t80) REVERT: B 490 ARG cc_start: 0.7965 (mtt90) cc_final: 0.6879 (tpm170) REVERT: B 737 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7782 (tpp) REVERT: B 767 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8312 (pp) REVERT: B 999 GLN cc_start: 0.8581 (tm-30) cc_final: 0.7889 (tm-30) outliers start: 20 outliers final: 12 residues processed: 94 average time/residue: 0.0891 time to fit residues: 12.1994 Evaluate side-chains 84 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 104 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.114683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.088404 restraints weight = 27953.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.089171 restraints weight = 16839.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.090050 restraints weight = 13414.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090293 restraints weight = 11264.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090468 restraints weight = 10695.991| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9375 Z= 0.170 Angle : 0.667 9.699 12751 Z= 0.334 Chirality : 0.046 0.329 1498 Planarity : 0.005 0.064 1615 Dihedral : 4.881 35.091 1241 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.85 % Favored : 88.97 % Rotamer: Outliers : 2.58 % Allowed : 19.52 % Favored : 77.90 % 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: -1.38 (0.24), residues: 1124 helix: 1.63 (0.33), residues: 263 sheet: 0.17 (0.43), residues: 143 loop : -2.31 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 980 TYR 0.011 0.001 TYR B 348 PHE 0.013 0.001 PHE B 556 TRP 0.008 0.001 TRP A 630 HIS 0.003 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 9349) covalent geometry : angle 0.65442 / 0.33 (12690) SS BOND : bond 0.00381 / 0.24 ( 17) SS BOND : angle 1.43924 / 0.91 ( 34) hydrogen bonds : bond 0.04201 / 2.87 ( 300) hydrogen bonds : angle 4.97441 / 3.47 ( 819) link_BETA1-4 : bond 0.00795 / 0.39 ( 4) link_BETA1-4 : angle 2.82409 / 1.49 ( 12) link_NAG-ASN : bond 0.00217 / 0.09 ( 5) link_NAG-ASN : angle 2.06100 / 1.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 777 GLU cc_start: 0.8168 (pt0) cc_final: 0.7878 (pt0) REVERT: A 833 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7768 (tp-100) REVERT: A 987 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8823 (tm-30) REVERT: B 415 ILE cc_start: 0.8381 (mp) cc_final: 0.7858 (tp) REVERT: B 446 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6876 (t80) REVERT: B 490 ARG cc_start: 0.7958 (mtt90) cc_final: 0.6885 (tpm170) REVERT: B 737 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7785 (tpp) REVERT: B 999 GLN cc_start: 0.8621 (tm-30) cc_final: 0.7945 (tm-30) outliers start: 26 outliers final: 19 residues processed: 92 average time/residue: 0.0927 time to fit residues: 12.3981 Evaluate side-chains 88 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 70 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1008 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.115296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089753 restraints weight = 28513.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090272 restraints weight = 18608.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090629 restraints weight = 15155.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090906 restraints weight = 13242.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091031 restraints weight = 12235.498| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9375 Z= 0.162 Angle : 0.668 10.483 12751 Z= 0.336 Chirality : 0.046 0.342 1498 Planarity : 0.004 0.053 1615 Dihedral : 4.844 31.550 1241 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.41 % Favored : 89.41 % Rotamer: Outliers : 2.48 % Allowed : 20.02 % Favored : 77.50 % 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: -1.35 (0.25), residues: 1124 helix: 1.73 (0.33), residues: 263 sheet: 0.09 (0.42), residues: 146 loop : -2.32 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.011 0.001 TYR B 492 PHE 0.012 0.001 PHE A 272 TRP 0.009 0.001 TRP A 630 HIS 0.002 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 9349) covalent geometry : angle 0.65584 / 0.33 (12690) SS BOND : bond 0.00390 / 0.24 ( 17) SS BOND : angle 1.55800 / 0.96 ( 34) hydrogen bonds : bond 0.04166 / 2.85 ( 300) hydrogen bonds : angle 4.91049 / 3.41 ( 819) link_BETA1-4 : bond 0.00786 / 0.39 ( 4) link_BETA1-4 : angle 2.80315 / 1.49 ( 12) link_NAG-ASN : bond 0.00232 / 0.10 ( 5) link_NAG-ASN : angle 2.03285 / 1.13 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.7675 (ttm) cc_final: 0.7298 (tpp) REVERT: A 773 LYS cc_start: 0.8936 (tptt) cc_final: 0.8401 (tptt) REVERT: A 987 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8843 (tm-30) REVERT: B 415 ILE cc_start: 0.8381 (mp) cc_final: 0.7886 (tp) REVERT: B 446 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6664 (t80) REVERT: B 490 ARG cc_start: 0.8051 (mtt90) cc_final: 0.6984 (tpm170) REVERT: B 737 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7717 (tpp) REVERT: B 770 GLU cc_start: 0.7857 (pt0) cc_final: 0.7522 (tt0) REVERT: B 999 GLN cc_start: 0.8569 (tm-30) cc_final: 0.7877 (tm-30) outliers start: 25 outliers final: 19 residues processed: 96 average time/residue: 0.0877 time to fit residues: 12.5226 Evaluate side-chains 91 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 748 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.116030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.090779 restraints weight = 28463.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090939 restraints weight = 18769.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.091432 restraints weight = 15695.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.091726 restraints weight = 13037.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.091904 restraints weight = 12187.653| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9375 Z= 0.135 Angle : 0.654 10.770 12751 Z= 0.326 Chirality : 0.045 0.350 1498 Planarity : 0.004 0.052 1615 Dihedral : 4.682 31.464 1241 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.32 % Favored : 89.50 % Rotamer: Outliers : 2.48 % Allowed : 20.12 % Favored : 77.40 % 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: -1.34 (0.25), residues: 1124 helix: 1.67 (0.33), residues: 269 sheet: 0.11 (0.43), residues: 144 loop : -2.32 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 762 TYR 0.011 0.001 TYR B 492 PHE 0.010 0.001 PHE A 131 TRP 0.010 0.001 TRP A 630 HIS 0.002 0.001 HIS A1055 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 9349) covalent geometry : angle 0.64214 / 0.32 (12690) SS BOND : bond 0.00349 / 0.22 ( 17) SS BOND : angle 1.47116 / 0.91 ( 34) hydrogen bonds : bond 0.03982 / 2.72 ( 300) hydrogen bonds : angle 4.82362 / 3.34 ( 819) link_BETA1-4 : bond 0.00781 / 0.39 ( 4) link_BETA1-4 : angle 2.75425 / 1.46 ( 12) link_NAG-ASN : bond 0.00257 / 0.12 ( 5) link_NAG-ASN : angle 1.97981 / 1.10 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8390 (tt) REVERT: A 777 GLU cc_start: 0.8113 (pt0) cc_final: 0.7842 (pt0) REVERT: A 987 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8848 (tm-30) REVERT: B 415 ILE cc_start: 0.8348 (mp) cc_final: 0.7855 (tp) REVERT: B 446 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6616 (t80) REVERT: B 490 ARG cc_start: 0.8044 (mtt90) cc_final: 0.7025 (tpm170) REVERT: B 737 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7755 (tpp) REVERT: B 752 GLN cc_start: 0.8912 (mp10) cc_final: 0.8678 (mp10) REVERT: B 770 GLU cc_start: 0.7812 (pt0) cc_final: 0.7453 (tt0) REVERT: B 999 GLN cc_start: 0.8557 (tm-30) cc_final: 0.7942 (tm-30) outliers start: 25 outliers final: 18 residues processed: 95 average time/residue: 0.0785 time to fit residues: 11.1998 Evaluate side-chains 93 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 0.2980 chunk 83 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.116980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.091672 restraints weight = 28447.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.091748 restraints weight = 18529.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.092408 restraints weight = 15230.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.092802 restraints weight = 12445.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.092943 restraints weight = 11770.023| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9375 Z= 0.119 Angle : 0.656 11.736 12751 Z= 0.325 Chirality : 0.046 0.346 1498 Planarity : 0.004 0.056 1615 Dihedral : 4.570 31.557 1240 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.79 % Favored : 90.04 % Rotamer: Outliers : 1.98 % Allowed : 20.91 % Favored : 77.11 % 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: -1.33 (0.25), residues: 1124 helix: 1.57 (0.33), residues: 269 sheet: 0.23 (0.45), residues: 136 loop : -2.25 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 980 TYR 0.011 0.001 TYR B 492 PHE 0.014 0.001 PHE A 756 TRP 0.012 0.001 TRP A 630 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9349) covalent geometry : angle 0.64436 / 0.32 (12690) SS BOND : bond 0.00305 / 0.19 ( 17) SS BOND : angle 1.39243 / 0.85 ( 34) hydrogen bonds : bond 0.03869 / 2.65 ( 300) hydrogen bonds : angle 4.73856 / 3.29 ( 819) link_BETA1-4 : bond 0.00780 / 0.39 ( 4) link_BETA1-4 : angle 2.73021 / 1.45 ( 12) link_NAG-ASN : bond 0.00258 / 0.12 ( 5) link_NAG-ASN : angle 1.94227 / 1.09 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8384 (tt) REVERT: A 770 GLU cc_start: 0.8464 (tt0) cc_final: 0.8208 (tt0) REVERT: A 987 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8857 (tm-30) REVERT: B 415 ILE cc_start: 0.8350 (mp) cc_final: 0.7850 (tp) REVERT: B 490 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7035 (tpm170) REVERT: B 737 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7768 (tpp) REVERT: B 752 GLN cc_start: 0.8910 (mp10) cc_final: 0.8674 (mp10) REVERT: B 770 GLU cc_start: 0.7812 (pt0) cc_final: 0.7437 (tt0) REVERT: B 999 GLN cc_start: 0.8561 (tm-30) cc_final: 0.7926 (tm-30) outliers start: 20 outliers final: 15 residues processed: 94 average time/residue: 0.0982 time to fit residues: 13.4212 Evaluate side-chains 89 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.117251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091870 restraints weight = 28572.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.092200 restraints weight = 18061.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092868 restraints weight = 14610.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093270 restraints weight = 12170.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.093409 restraints weight = 11277.183| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9375 Z= 0.120 Angle : 0.655 11.788 12751 Z= 0.325 Chirality : 0.046 0.343 1498 Planarity : 0.004 0.052 1615 Dihedral : 4.430 29.166 1238 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.52 % Favored : 90.30 % Rotamer: Outliers : 1.78 % Allowed : 21.01 % Favored : 77.21 % 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: -1.31 (0.25), residues: 1124 helix: 1.61 (0.33), residues: 265 sheet: 0.25 (0.45), residues: 136 loop : -2.23 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 762 TYR 0.012 0.001 TYR B 492 PHE 0.023 0.001 PHE A 272 TRP 0.013 0.001 TRP A 630 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9349) covalent geometry : angle 0.64377 / 0.32 (12690) SS BOND : bond 0.00353 / 0.22 ( 17) SS BOND : angle 1.43514 / 0.87 ( 34) hydrogen bonds : bond 0.03771 / 2.58 ( 300) hydrogen bonds : angle 4.67979 / 3.25 ( 819) link_BETA1-4 : bond 0.00755 / 0.38 ( 4) link_BETA1-4 : angle 2.68899 / 1.42 ( 12) link_NAG-ASN : bond 0.00252 / 0.12 ( 5) link_NAG-ASN : angle 1.91084 / 1.07 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.7853 (tpt) cc_final: 0.7459 (tpp) REVERT: A 300 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8388 (tt) REVERT: A 622 HIS cc_start: 0.4252 (p-80) cc_final: 0.3958 (p-80) REVERT: A 745 GLU cc_start: 0.8363 (pm20) cc_final: 0.8161 (mt-10) REVERT: A 987 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8820 (tm-30) REVERT: B 415 ILE cc_start: 0.8334 (mp) cc_final: 0.7816 (tp) REVERT: B 490 ARG cc_start: 0.7996 (mtt90) cc_final: 0.6987 (tpm170) REVERT: B 737 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7666 (tpp) REVERT: B 770 GLU cc_start: 0.7815 (pt0) cc_final: 0.7461 (tt0) REVERT: B 999 GLN cc_start: 0.8528 (tm-30) cc_final: 0.7885 (tm-30) outliers start: 18 outliers final: 16 residues processed: 90 average time/residue: 0.0906 time to fit residues: 11.9178 Evaluate side-chains 90 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 1009 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 0.0980 chunk 80 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 GLN ** 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 = 0.3914 r_free = 0.3914 target = 0.116177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091074 restraints weight = 28002.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.091208 restraints weight = 17736.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.091834 restraints weight = 14888.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092180 restraints weight = 12569.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.092352 restraints weight = 11479.989| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9375 Z= 0.137 Angle : 0.670 12.519 12751 Z= 0.336 Chirality : 0.046 0.354 1498 Planarity : 0.004 0.049 1615 Dihedral : 4.452 29.347 1238 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.70 % Favored : 90.12 % Rotamer: Outliers : 1.98 % Allowed : 21.21 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.38 (0.25), residues: 1124 helix: 1.58 (0.33), residues: 264 sheet: 0.15 (0.45), residues: 136 loop : -2.28 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 762 TYR 0.012 0.001 TYR B 492 PHE 0.025 0.001 PHE A 756 TRP 0.012 0.001 TRP A 630 HIS 0.002 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9349) covalent geometry : angle 0.65912 / 0.33 (12690) SS BOND : bond 0.00351 / 0.22 ( 17) SS BOND : angle 1.50461 / 0.91 ( 34) hydrogen bonds : bond 0.03821 / 2.62 ( 300) hydrogen bonds : angle 4.73574 / 3.28 ( 819) link_BETA1-4 : bond 0.00767 / 0.38 ( 4) link_BETA1-4 : angle 2.67505 / 1.42 ( 12) link_NAG-ASN : bond 0.00220 / 0.09 ( 5) link_NAG-ASN : angle 1.89251 / 1.05 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1448.85 seconds wall clock time: 25 minutes 53.90 seconds (1553.90 seconds total)