Starting phenix.real_space_refine on Sat Sep 12 14:21:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xnx_22272/09_2026/6xnx_22272.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xnx_22272/09_2026/6xnx_22272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xnx_22272/09_2026/6xnx_22272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xnx_22272/09_2026/6xnx_22272.map" model { file = "/net/cci-nas-00/data/ceres_data/6xnx_22272/09_2026/6xnx_22272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xnx_22272/09_2026/6xnx_22272.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xnx_22272/09_2026/6xnx_22272.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xnx_22272/09_2026/6xnx_22272.cif" } resolution = 2.7 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= 0.006 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 110 5.49 5 Mg 4 5.21 5 S 106 5.16 5 C 10116 2.51 5 N 2888 2.21 5 O 3314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16540 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4407 Classifications: {'peptide': 549} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 523} Chain: "B" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2678 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 19, 'TRANS': 322} Chain breaks: 2 Chain: "C" Number of atoms: 4401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4401 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} Chain: "D" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2688 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain breaks: 2 Chain: "x" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 644 Classifications: {'DNA': 32} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "y" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 564 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "I" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "J" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 288 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "L" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "M" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2078 SG CYS A 727 67.283 86.310 61.612 1.00 41.02 S ATOM 2099 SG CYS A 730 67.279 89.825 63.913 1.00 40.07 S ATOM 9163 SG CYS C 727 66.679 22.583 62.396 1.00 40.59 S ATOM 9184 SG CYS C 730 66.702 19.139 64.824 1.00 40.18 S Time building chain proxies: 3.49, per 1000 atoms: 0.21 Number of scatterers: 16540 At special positions: 0 Unit cell: (134.4, 109.2, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 110 15.00 Mg 4 11.99 O 3314 8.00 N 2888 7.00 C 10116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 606.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1103 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 727 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " Number of angles added : 4 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 20 sheets defined 35.9% alpha, 22.3% beta 54 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 492 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.903A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 824 through 840 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.675A pdb=" N GLU A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 895 Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 953 through 957 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.645A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 996 through 1003 removed outlier: 3.606A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.803A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 492 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.689A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 581 removed outlier: 4.873A pdb=" N GLU C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP C 573 " --> pdb=" O ASP C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 684 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 Processing helix chain 'C' and resid 822 through 840 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 908 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 958 through 975 Processing helix chain 'C' and resid 979 through 995 removed outlier: 4.805A pdb=" N MET C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 519 removed outlier: 4.854A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519 removed outlier: 4.854A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.719A pdb=" N PHE B 24 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 8 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N PHE B 343 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.150A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.014A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AB1, first strand: chain 'C' and resid 517 through 519 removed outlier: 6.538A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 517 through 519 removed outlier: 6.538A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 631 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS C 639 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS C 633 " --> pdb=" O ASN C 637 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN C 637 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.431A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 22 through 24 removed outlier: 4.795A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.160A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG D 123 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL D 112 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR D 125 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N MET D 110 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS D 127 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR D 108 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.351A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.791A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 267 removed outlier: 6.882A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 277 through 279 682 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 274 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4859 1.33 - 1.45: 3758 1.45 - 1.57: 8146 1.57 - 1.69: 217 1.69 - 1.81: 164 Bond restraints: 17144 Sorted by residual: bond pdb=" CA LEU C 657 " pdb=" CB LEU C 657 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.39e-02 5.18e+03 2.52e+01 bond pdb=" N9 DA L 20 " pdb=" C4 DA L 20 " ideal model delta sigma weight residual 1.374 1.347 0.027 6.00e-03 2.78e+04 2.06e+01 bond pdb=" O3' DA y 30 " pdb=" P DC y 31 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.20e-02 6.94e+03 2.02e+01 bond pdb=" N9 DA M 20 " pdb=" C4 DA M 20 " ideal model delta sigma weight residual 1.374 1.349 0.025 6.00e-03 2.78e+04 1.71e+01 bond pdb=" C3' DG M 23 " pdb=" O3' DG M 23 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.55e+01 ... (remaining 17139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 23142 2.54 - 5.09: 493 5.09 - 7.63: 14 7.63 - 10.17: 3 10.17 - 12.72: 1 Bond angle restraints: 23653 Sorted by residual: angle pdb=" C4' DG y 35 " pdb=" O4' DG y 35 " pdb=" C1' DG y 35 " ideal model delta sigma weight residual 110.10 103.10 7.00 1.00e+00 1.00e+00 4.90e+01 angle pdb=" C4' DG x 46 " pdb=" O4' DG x 46 " pdb=" C1' DG x 46 " ideal model delta sigma weight residual 110.10 103.26 6.84 1.00e+00 1.00e+00 4.68e+01 angle pdb=" C ASP A 834 " pdb=" CA ASP A 834 " pdb=" CB ASP A 834 " ideal model delta sigma weight residual 110.96 101.35 9.61 1.54e+00 4.22e-01 3.89e+01 angle pdb=" CG ARG A 773 " pdb=" CD ARG A 773 " pdb=" NE ARG A 773 " ideal model delta sigma weight residual 112.00 99.28 12.72 2.20e+00 2.07e-01 3.34e+01 angle pdb=" O4' DT x 45 " pdb=" C4' DT x 45 " pdb=" C3' DT x 45 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.86e+01 ... (remaining 23648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.58: 9269 33.58 - 67.15: 704 67.15 - 100.73: 18 100.73 - 134.30: 0 134.30 - 167.88: 3 Dihedral angle restraints: 9994 sinusoidal: 4816 harmonic: 5178 Sorted by residual: dihedral pdb=" CA GLN A 520 " pdb=" C GLN A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta harmonic sigma weight residual 180.00 150.25 29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA TYR A 725 " pdb=" C TYR A 725 " pdb=" N ILE A 726 " pdb=" CA ILE A 726 " ideal model delta harmonic sigma weight residual -180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA TYR C 725 " pdb=" C TYR C 725 " pdb=" N ILE C 726 " pdb=" CA ILE C 726 " ideal model delta harmonic sigma weight residual 180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 9991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2091 0.079 - 0.157: 412 0.157 - 0.236: 71 0.236 - 0.315: 4 0.315 - 0.393: 6 Chirality restraints: 2584 Sorted by residual: chirality pdb=" C3' DT x 45 " pdb=" C4' DT x 45 " pdb=" O3' DT x 45 " pdb=" C2' DT x 45 " both_signs ideal model delta sigma weight residual False -2.73 -2.34 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA TRP B 317 " pdb=" N TRP B 317 " pdb=" C TRP B 317 " pdb=" CB TRP B 317 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ASP A 792 " pdb=" N ASP A 792 " pdb=" C ASP A 792 " pdb=" CB ASP A 792 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 2581 not shown) Planarity restraints: 2643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 233 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU D 233 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU D 233 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR D 234 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT x 43 " 0.043 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" N1 DT x 43 " -0.043 2.00e-02 2.50e+03 pdb=" C2 DT x 43 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT x 43 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DT x 43 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DT x 43 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT x 43 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT x 43 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT x 43 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT x 43 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA y 30 " 0.039 2.00e-02 2.50e+03 1.87e-02 9.64e+00 pdb=" N9 DA y 30 " -0.040 2.00e-02 2.50e+03 pdb=" C8 DA y 30 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA y 30 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DA y 30 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DA y 30 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA y 30 " 0.023 2.00e-02 2.50e+03 pdb=" N1 DA y 30 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA y 30 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA y 30 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DA y 30 " -0.007 2.00e-02 2.50e+03 ... (remaining 2640 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 94 2.36 - 2.99: 9762 2.99 - 3.63: 29509 3.63 - 4.26: 48409 4.26 - 4.90: 74533 Nonbonded interactions: 162307 Sorted by model distance: nonbonded pdb=" O GLY A 601 " pdb="MG MG A1101 " model vdw 1.724 2.170 nonbonded pdb=" OP2 DC y 36 " pdb="MG MG A1101 " model vdw 1.901 2.170 nonbonded pdb=" O GLY C 601 " pdb="MG MG x 101 " model vdw 1.937 2.170 nonbonded pdb=" OE2 GLU A 662 " pdb="MG MG A1102 " model vdw 1.999 2.170 nonbonded pdb=" O ASN D 117 " pdb=" OD1 ASN D 117 " model vdw 2.015 3.040 ... (remaining 162302 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 460 through 1007 or resid 1102 through 1103)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 335 or resid 339 through 350)) selection = (chain 'D' and (resid 1 through 335 or resid 339 through 350)) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.580 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.013 0.227 17152 Z= 0.668 Angle : 0.993 48.066 23657 Z= 0.576 Chirality : 0.066 0.393 2584 Planarity : 0.004 0.039 2643 Dihedral : 20.133 167.880 6658 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.20 % Rotamer: Outliers : 2.35 % Allowed : 11.90 % Favored : 85.75 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 1.14 % 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: -4.23 (0.16), residues: 1766 helix: -2.27 (0.17), residues: 565 sheet: -3.52 (0.24), residues: 284 loop : -2.93 (0.17), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 773 TYR 0.015 0.002 TYR A 928 PHE 0.017 0.002 PHE D 206 TRP 0.025 0.003 TRP B 317 HIS 0.008 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.01289 / 0.66 (17144) covalent geometry : angle 0.83665 / 0.57 (23653) hydrogen bonds : bond 0.13390 / 9.03 ( 775) hydrogen bonds : angle 8.15520 / 5.70 ( 2158) metal coordination : bond 0.13049 / 6.66 ( 8) metal coordination : angle 41.10463 / 20.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 743 PHE cc_start: 0.7846 (m-80) cc_final: 0.7333 (m-80) REVERT: A 827 LYS cc_start: 0.8196 (tptm) cc_final: 0.7994 (tttp) REVERT: A 861 GLU cc_start: 0.6735 (tt0) cc_final: 0.6513 (mm-30) REVERT: A 949 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7866 (ttp-170) REVERT: B 322 MET cc_start: 0.7599 (mtp) cc_final: 0.7341 (mtm) REVERT: C 571 GLU cc_start: 0.7693 (tt0) cc_final: 0.7440 (tt0) REVERT: C 627 MET cc_start: 0.9041 (mmm) cc_final: 0.8667 (mmm) REVERT: C 659 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8395 (mt) REVERT: C 691 MET cc_start: 0.8335 (mtp) cc_final: 0.7884 (mtm) REVERT: C 701 ILE cc_start: 0.9102 (mt) cc_final: 0.8902 (mm) REVERT: C 780 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.7987 (t) REVERT: C 848 MET cc_start: 0.7431 (ttp) cc_final: 0.7209 (ttp) REVERT: D 237 ARG cc_start: 0.7410 (ttm110) cc_final: 0.7106 (ttm-80) REVERT: D 269 ASP cc_start: 0.7100 (m-30) cc_final: 0.6811 (m-30) REVERT: D 316 ILE cc_start: 0.8332 (mp) cc_final: 0.8100 (mt) outliers start: 37 outliers final: 19 residues processed: 330 average time/residue: 0.6254 time to fit residues: 229.0654 Evaluate side-chains 209 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 738 SER Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 780 SER Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 HIS A 744 HIS A 763 ASN ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 54 HIS B 101 ASN B 166 GLN B 227 ASN C 473 ASN D 27 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.154132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130461 restraints weight = 19801.510| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.49 r_work: 0.3458 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 17152 Z= 0.220 Angle : 0.765 18.497 23657 Z= 0.406 Chirality : 0.049 0.389 2584 Planarity : 0.005 0.068 2643 Dihedral : 22.557 177.732 3191 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 4.52 % Allowed : 17.24 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -2.89 (0.18), residues: 1766 helix: -0.94 (0.19), residues: 573 sheet: -3.22 (0.24), residues: 298 loop : -2.06 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 855 TYR 0.029 0.002 TYR A 725 PHE 0.019 0.002 PHE B 30 TRP 0.015 0.003 TRP A 893 HIS 0.009 0.002 HIS C 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (17144) covalent geometry : angle 0.73935 / 0.40 (23653) hydrogen bonds : bond 0.05008 / 3.31 ( 775) hydrogen bonds : angle 6.53202 / 4.59 ( 2158) metal coordination : bond 0.07766 / 4.17 ( 8) metal coordination : angle 15.18990 / 7.83 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 253 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 743 PHE cc_start: 0.8160 (m-80) cc_final: 0.7625 (m-80) REVERT: A 823 LYS cc_start: 0.7795 (tppt) cc_final: 0.7260 (tppt) REVERT: A 861 GLU cc_start: 0.7344 (tt0) cc_final: 0.6934 (mm-30) REVERT: A 923 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7581 (mmtm) REVERT: B 49 ASP cc_start: 0.7937 (m-30) cc_final: 0.7626 (m-30) REVERT: B 286 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8361 (m) REVERT: B 322 MET cc_start: 0.7900 (mtp) cc_final: 0.7667 (mtm) REVERT: B 334 ASP cc_start: 0.5678 (t70) cc_final: 0.5196 (t0) REVERT: C 627 MET cc_start: 0.9045 (mmm) cc_final: 0.8736 (mmm) REVERT: C 659 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8767 (mt) REVERT: C 691 MET cc_start: 0.8456 (mtp) cc_final: 0.7905 (mtm) REVERT: C 818 HIS cc_start: 0.6082 (m90) cc_final: 0.5851 (m170) REVERT: D 148 ARG cc_start: 0.8238 (mmt90) cc_final: 0.8013 (mmm-85) REVERT: D 193 THR cc_start: 0.8494 (m) cc_final: 0.8164 (p) REVERT: D 237 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7269 (ttm-80) REVERT: D 262 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8721 (mp) REVERT: D 314 SER cc_start: 0.8636 (t) cc_final: 0.8430 (p) REVERT: D 316 ILE cc_start: 0.8472 (mp) cc_final: 0.8240 (mt) REVERT: D 349 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7307 (ttm110) outliers start: 71 outliers final: 18 residues processed: 301 average time/residue: 0.5181 time to fit residues: 175.9641 Evaluate side-chains 214 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 915 ARG Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 182 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 HIS A 763 ASN ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN C1006 HIS D 16 GLN D 27 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126328 restraints weight = 20072.908| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.50 r_work: 0.3421 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.145 17152 Z= 0.255 Angle : 0.729 13.909 23657 Z= 0.390 Chirality : 0.048 0.360 2584 Planarity : 0.005 0.082 2643 Dihedral : 22.575 177.180 3175 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 4.90 % Allowed : 19.59 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -2.33 (0.18), residues: 1766 helix: -0.44 (0.20), residues: 588 sheet: -2.99 (0.23), residues: 308 loop : -1.70 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 529 TYR 0.024 0.002 TYR A 725 PHE 0.020 0.002 PHE B 24 TRP 0.015 0.002 TRP D 317 HIS 0.011 0.002 HIS C 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 (17144) covalent geometry : angle 0.71364 / 0.39 (23653) hydrogen bonds : bond 0.05091 / 3.43 ( 775) hydrogen bonds : angle 6.22970 / 4.40 ( 2158) metal coordination : bond 0.06913 / 4.04 ( 8) metal coordination : angle 11.41533 / 6.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 227 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 ASP cc_start: 0.8428 (t0) cc_final: 0.8181 (t0) REVERT: A 743 PHE cc_start: 0.8224 (m-80) cc_final: 0.7718 (m-80) REVERT: A 818 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.6751 (m-70) REVERT: A 861 GLU cc_start: 0.7460 (tt0) cc_final: 0.7035 (mm-30) REVERT: B 49 ASP cc_start: 0.8016 (m-30) cc_final: 0.7692 (m-30) REVERT: B 77 THR cc_start: 0.8181 (m) cc_final: 0.7910 (p) REVERT: B 188 GLU cc_start: 0.6983 (mp0) cc_final: 0.6657 (tp30) REVERT: B 322 MET cc_start: 0.8022 (mtp) cc_final: 0.7759 (mtm) REVERT: B 334 ASP cc_start: 0.5741 (t70) cc_final: 0.5232 (t0) REVERT: C 659 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8880 (mt) REVERT: C 682 MET cc_start: 0.8847 (mtp) cc_final: 0.8550 (mtm) REVERT: C 691 MET cc_start: 0.8413 (mtp) cc_final: 0.8029 (mtm) REVERT: D 105 ASP cc_start: 0.7121 (p0) cc_final: 0.6779 (p0) REVERT: D 193 THR cc_start: 0.8481 (m) cc_final: 0.8109 (p) REVERT: D 237 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7378 (ttm-80) REVERT: D 262 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8772 (mp) REVERT: D 289 LEU cc_start: 0.8907 (tp) cc_final: 0.8642 (tm) REVERT: D 298 GLU cc_start: 0.7552 (mp0) cc_final: 0.7210 (mp0) outliers start: 77 outliers final: 27 residues processed: 280 average time/residue: 0.4898 time to fit residues: 155.9115 Evaluate side-chains 225 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 111 optimal weight: 0.0980 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 0.0060 chunk 159 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 633 HIS C 818 HIS D 23 ASN D 27 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.155390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131869 restraints weight = 19806.664| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.50 r_work: 0.3500 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 17152 Z= 0.170 Angle : 0.669 11.219 23657 Z= 0.361 Chirality : 0.046 0.358 2584 Planarity : 0.005 0.066 2643 Dihedral : 22.504 179.396 3175 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 4.90 % Allowed : 20.48 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -1.95 (0.19), residues: 1766 helix: -0.12 (0.20), residues: 582 sheet: -2.87 (0.23), residues: 326 loop : -1.39 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 529 TYR 0.022 0.002 TYR C 725 PHE 0.018 0.002 PHE B 24 TRP 0.013 0.002 TRP B 307 HIS 0.007 0.001 HIS C 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (17144) covalent geometry : angle 0.66168 / 0.36 (23653) hydrogen bonds : bond 0.04169 / 2.78 ( 775) hydrogen bonds : angle 6.04858 / 4.29 ( 2158) metal coordination : bond 0.04863 / 2.60 ( 8) metal coordination : angle 7.49201 / 4.12 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 230 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7782 (t0) cc_final: 0.7461 (t0) REVERT: A 743 PHE cc_start: 0.8130 (m-80) cc_final: 0.7671 (m-80) REVERT: B 49 ASP cc_start: 0.7922 (m-30) cc_final: 0.7638 (m-30) REVERT: B 322 MET cc_start: 0.7892 (mtp) cc_final: 0.7670 (mtm) REVERT: C 627 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8646 (mmm) REVERT: C 686 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: C 691 MET cc_start: 0.8437 (mtp) cc_final: 0.8011 (mtm) REVERT: D 105 ASP cc_start: 0.7146 (p0) cc_final: 0.6822 (p0) REVERT: D 193 THR cc_start: 0.8520 (m) cc_final: 0.8210 (p) REVERT: D 202 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6688 (t70) REVERT: D 237 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7473 (ttm-80) REVERT: D 262 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8537 (mp) REVERT: D 280 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7174 (tp30) REVERT: D 289 LEU cc_start: 0.8886 (tp) cc_final: 0.8673 (tm) outliers start: 77 outliers final: 22 residues processed: 284 average time/residue: 0.4850 time to fit residues: 156.4896 Evaluate side-chains 227 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 627 MET Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 82 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 184 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 830 GLN ** C 744 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 HIS D 23 ASN D 27 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.152275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128491 restraints weight = 20102.320| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.49 r_work: 0.3440 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 17152 Z= 0.225 Angle : 0.691 10.408 23657 Z= 0.371 Chirality : 0.047 0.359 2584 Planarity : 0.005 0.068 2643 Dihedral : 22.432 179.481 3171 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 4.26 % Allowed : 22.20 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -1.76 (0.19), residues: 1766 helix: -0.05 (0.20), residues: 588 sheet: -2.77 (0.24), residues: 318 loop : -1.23 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 349 TYR 0.024 0.002 TYR C 725 PHE 0.013 0.002 PHE B 48 TRP 0.014 0.002 TRP B 317 HIS 0.006 0.002 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (17144) covalent geometry : angle 0.68463 / 0.37 (23653) hydrogen bonds : bond 0.04575 / 3.08 ( 775) hydrogen bonds : angle 5.96878 / 4.25 ( 2158) metal coordination : bond 0.05522 / 3.14 ( 8) metal coordination : angle 6.99970 / 3.84 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 210 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7851 (t0) cc_final: 0.7525 (t0) REVERT: A 731 ASP cc_start: 0.7911 (p0) cc_final: 0.7522 (p0) REVERT: A 743 PHE cc_start: 0.8133 (m-80) cc_final: 0.7688 (m-80) REVERT: A 747 THR cc_start: 0.8497 (m) cc_final: 0.8259 (p) REVERT: A 923 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7311 (mtpp) REVERT: B 49 ASP cc_start: 0.7934 (m-30) cc_final: 0.7627 (m-30) REVERT: B 322 MET cc_start: 0.7987 (mtp) cc_final: 0.7728 (mtm) REVERT: C 659 LEU cc_start: 0.9195 (mt) cc_final: 0.8935 (mt) REVERT: C 691 MET cc_start: 0.8494 (mtp) cc_final: 0.8114 (mtm) REVERT: D 105 ASP cc_start: 0.7179 (p0) cc_final: 0.6875 (p0) REVERT: D 143 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: D 193 THR cc_start: 0.8562 (m) cc_final: 0.8216 (p) REVERT: D 202 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6654 (t70) REVERT: D 237 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7479 (ttm-80) REVERT: D 262 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8534 (mp) REVERT: D 285 MET cc_start: 0.8826 (mmm) cc_final: 0.8582 (mmm) REVERT: D 289 LEU cc_start: 0.8880 (tp) cc_final: 0.8621 (tm) outliers start: 67 outliers final: 34 residues processed: 259 average time/residue: 0.5008 time to fit residues: 147.9048 Evaluate side-chains 233 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 177 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 151 optimal weight: 0.0170 chunk 85 optimal weight: 3.9990 chunk 26 optimal weight: 0.0070 chunk 30 optimal weight: 7.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 830 GLN C 647 ASN C 818 HIS D 23 ASN D 27 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.156350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133040 restraints weight = 20118.703| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.50 r_work: 0.3501 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 17152 Z= 0.163 Angle : 0.651 10.175 23657 Z= 0.354 Chirality : 0.046 0.354 2584 Planarity : 0.005 0.065 2643 Dihedral : 22.343 178.005 3171 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 5.03 % Allowed : 22.52 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -1.61 (0.19), residues: 1766 helix: 0.08 (0.21), residues: 581 sheet: -2.66 (0.25), residues: 305 loop : -1.17 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 349 TYR 0.025 0.002 TYR C 586 PHE 0.013 0.002 PHE B 30 TRP 0.012 0.002 TRP B 307 HIS 0.007 0.001 HIS C 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (17144) covalent geometry : angle 0.64709 / 0.35 (23653) hydrogen bonds : bond 0.04021 / 2.69 ( 775) hydrogen bonds : angle 5.87181 / 4.18 ( 2158) metal coordination : bond 0.03601 / 1.91 ( 8) metal coordination : angle 5.17518 / 2.93 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 220 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7779 (t0) cc_final: 0.7455 (t0) REVERT: A 731 ASP cc_start: 0.7865 (p0) cc_final: 0.7461 (p0) REVERT: A 743 PHE cc_start: 0.8075 (m-80) cc_final: 0.7708 (m-80) REVERT: A 818 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.6674 (m-70) REVERT: A 923 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7187 (mtpp) REVERT: B 49 ASP cc_start: 0.7774 (m-30) cc_final: 0.7477 (m-30) REVERT: B 322 MET cc_start: 0.7849 (mtp) cc_final: 0.7628 (mtm) REVERT: C 686 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: C 691 MET cc_start: 0.8476 (mtp) cc_final: 0.8092 (mtm) REVERT: C 784 PHE cc_start: 0.8200 (t80) cc_final: 0.7814 (t80) REVERT: D 105 ASP cc_start: 0.7180 (p0) cc_final: 0.6836 (p0) REVERT: D 193 THR cc_start: 0.8516 (m) cc_final: 0.8195 (p) REVERT: D 202 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6686 (t70) REVERT: D 237 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7444 (ttm-80) REVERT: D 262 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8514 (mp) REVERT: D 280 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7033 (tp30) REVERT: D 289 LEU cc_start: 0.8824 (tp) cc_final: 0.8604 (tm) REVERT: D 298 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7224 (mp0) outliers start: 79 outliers final: 30 residues processed: 276 average time/residue: 0.5057 time to fit residues: 158.9112 Evaluate side-chains 236 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.0040 chunk 13 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN D 23 ASN D 27 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.155932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132504 restraints weight = 20125.477| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.50 r_work: 0.3495 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 17152 Z= 0.177 Angle : 0.661 10.428 23657 Z= 0.355 Chirality : 0.046 0.356 2584 Planarity : 0.005 0.059 2643 Dihedral : 22.324 177.644 3170 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.30 % Rotamer: Outliers : 3.82 % Allowed : 23.98 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -1.53 (0.19), residues: 1766 helix: 0.13 (0.21), residues: 580 sheet: -2.57 (0.25), residues: 305 loop : -1.12 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 703 TYR 0.022 0.002 TYR C 725 PHE 0.012 0.002 PHE B 30 TRP 0.012 0.002 TRP B 307 HIS 0.006 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (17144) covalent geometry : angle 0.65746 / 0.35 (23653) hydrogen bonds : bond 0.04118 / 2.78 ( 775) hydrogen bonds : angle 5.83070 / 4.15 ( 2158) metal coordination : bond 0.03834 / 2.09 ( 8) metal coordination : angle 5.36555 / 3.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7788 (t0) cc_final: 0.7451 (t0) REVERT: A 731 ASP cc_start: 0.7823 (p0) cc_final: 0.7497 (p0) REVERT: A 818 HIS cc_start: 0.7633 (OUTLIER) cc_final: 0.6693 (m-70) REVERT: A 923 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7259 (mtpp) REVERT: B 49 ASP cc_start: 0.7743 (m-30) cc_final: 0.7478 (m-30) REVERT: B 322 MET cc_start: 0.7851 (mtp) cc_final: 0.7629 (mtm) REVERT: C 686 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: C 691 MET cc_start: 0.8519 (mtp) cc_final: 0.8202 (mtm) REVERT: C 784 PHE cc_start: 0.8221 (t80) cc_final: 0.7811 (t80) REVERT: C 827 LYS cc_start: 0.8434 (tttt) cc_final: 0.7851 (tttm) REVERT: D 143 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: D 202 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6693 (t70) REVERT: D 227 ASN cc_start: 0.8089 (t0) cc_final: 0.7863 (t0) REVERT: D 237 ARG cc_start: 0.7701 (ttm110) cc_final: 0.7426 (ttm-80) REVERT: D 262 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8516 (mp) REVERT: D 280 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7023 (tp30) REVERT: D 289 LEU cc_start: 0.8846 (tp) cc_final: 0.8580 (tm) outliers start: 60 outliers final: 29 residues processed: 262 average time/residue: 0.5276 time to fit residues: 156.4576 Evaluate side-chains 235 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 6 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN D 23 ASN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.153844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130016 restraints weight = 20215.525| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.51 r_work: 0.3461 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 17152 Z= 0.207 Angle : 0.682 12.942 23657 Z= 0.363 Chirality : 0.047 0.357 2584 Planarity : 0.005 0.057 2643 Dihedral : 22.342 177.183 3170 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 4.01 % Allowed : 24.36 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -1.47 (0.20), residues: 1766 helix: 0.16 (0.21), residues: 581 sheet: -2.56 (0.25), residues: 312 loop : -1.05 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 349 TYR 0.024 0.002 TYR C 725 PHE 0.013 0.002 PHE B 48 TRP 0.012 0.002 TRP B 317 HIS 0.006 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (17144) covalent geometry : angle 0.67820 / 0.36 (23653) hydrogen bonds : bond 0.04343 / 2.93 ( 775) hydrogen bonds : angle 5.83872 / 4.16 ( 2158) metal coordination : bond 0.04423 / 2.49 ( 8) metal coordination : angle 5.74519 / 3.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 529 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7416 (ttp-170) REVERT: A 531 ASP cc_start: 0.7811 (t0) cc_final: 0.7502 (t0) REVERT: A 731 ASP cc_start: 0.7860 (p0) cc_final: 0.7525 (p0) REVERT: A 743 PHE cc_start: 0.7948 (m-10) cc_final: 0.7730 (m-10) REVERT: A 818 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.6774 (m-70) REVERT: A 828 ARG cc_start: 0.7894 (tpp80) cc_final: 0.7601 (ttm-80) REVERT: A 923 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7413 (mtpp) REVERT: B 49 ASP cc_start: 0.7723 (m-30) cc_final: 0.7489 (m-30) REVERT: B 322 MET cc_start: 0.7889 (mtp) cc_final: 0.7663 (mtm) REVERT: C 686 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: C 691 MET cc_start: 0.8585 (mtp) cc_final: 0.8272 (mtm) REVERT: C 827 LYS cc_start: 0.8447 (tttt) cc_final: 0.7873 (tttm) REVERT: D 143 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: D 179 LEU cc_start: 0.8494 (mp) cc_final: 0.8290 (mt) REVERT: D 202 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6716 (t70) REVERT: D 227 ASN cc_start: 0.8033 (t0) cc_final: 0.7808 (t0) REVERT: D 237 ARG cc_start: 0.7744 (ttm110) cc_final: 0.7473 (ttm-80) REVERT: D 262 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8517 (mp) REVERT: D 280 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7033 (tp30) REVERT: D 289 LEU cc_start: 0.8897 (tp) cc_final: 0.8593 (tm) outliers start: 63 outliers final: 31 residues processed: 260 average time/residue: 0.4992 time to fit residues: 147.7871 Evaluate side-chains 237 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 839 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 0.0020 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN B 173 ASN C 525 ASN C 647 ASN D 23 ASN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.133119 restraints weight = 20226.915| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.51 r_work: 0.3504 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17152 Z= 0.169 Angle : 0.671 11.286 23657 Z= 0.359 Chirality : 0.046 0.353 2584 Planarity : 0.004 0.054 2643 Dihedral : 22.281 176.016 3170 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 2.86 % Allowed : 25.89 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: -1.42 (0.19), residues: 1766 helix: 0.20 (0.21), residues: 579 sheet: -2.51 (0.25), residues: 305 loop : -1.05 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 349 TYR 0.023 0.002 TYR C 725 PHE 0.013 0.002 PHE B 30 TRP 0.012 0.002 TRP C 893 HIS 0.005 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (17144) covalent geometry : angle 0.66780 / 0.36 (23653) hydrogen bonds : bond 0.04039 / 2.71 ( 775) hydrogen bonds : angle 5.79816 / 4.14 ( 2158) metal coordination : bond 0.03271 / 1.77 ( 8) metal coordination : angle 4.78710 / 2.75 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.454 Fit side-chains REVERT: A 529 ARG cc_start: 0.7540 (mtp180) cc_final: 0.7319 (ttp-170) REVERT: A 531 ASP cc_start: 0.7690 (t0) cc_final: 0.7342 (t0) REVERT: A 731 ASP cc_start: 0.7832 (p0) cc_final: 0.7502 (p0) REVERT: A 743 PHE cc_start: 0.7846 (m-10) cc_final: 0.7612 (m-10) REVERT: A 877 GLU cc_start: 0.7836 (tp30) cc_final: 0.7567 (tp30) REVERT: A 923 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7224 (mtpp) REVERT: A 929 GLU cc_start: 0.6771 (tm-30) cc_final: 0.6409 (tm-30) REVERT: B 322 MET cc_start: 0.7791 (mtp) cc_final: 0.7586 (mtm) REVERT: B 344 TYR cc_start: 0.8491 (m-80) cc_final: 0.8230 (m-10) REVERT: C 686 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: C 691 MET cc_start: 0.8563 (mtp) cc_final: 0.8230 (mtm) REVERT: C 743 PHE cc_start: 0.8557 (m-80) cc_final: 0.8152 (m-80) REVERT: C 784 PHE cc_start: 0.8154 (t80) cc_final: 0.7712 (t80) REVERT: C 827 LYS cc_start: 0.8456 (tttt) cc_final: 0.7895 (tttm) REVERT: D 143 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: D 237 ARG cc_start: 0.7718 (ttm110) cc_final: 0.7473 (ttm-80) REVERT: D 262 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8497 (mp) REVERT: D 264 THR cc_start: 0.8421 (t) cc_final: 0.8053 (t) REVERT: D 280 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6941 (tp30) REVERT: D 289 LEU cc_start: 0.8882 (tp) cc_final: 0.8453 (tm) REVERT: D 349 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7251 (mmt90) outliers start: 45 outliers final: 25 residues processed: 248 average time/residue: 0.5026 time to fit residues: 140.8281 Evaluate side-chains 234 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 262 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 146 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 41 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 740 ASN ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN D 23 ASN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.156842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133547 restraints weight = 20199.911| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.51 r_work: 0.3509 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17152 Z= 0.173 Angle : 0.673 11.223 23657 Z= 0.359 Chirality : 0.046 0.355 2584 Planarity : 0.005 0.068 2643 Dihedral : 22.247 175.347 3170 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 2.42 % Allowed : 26.78 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 (0.19), residues: 1766 helix: 0.25 (0.21), residues: 577 sheet: -2.43 (0.26), residues: 281 loop : -1.04 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 703 TYR 0.023 0.002 TYR C 725 PHE 0.016 0.002 PHE A 911 TRP 0.011 0.002 TRP B 317 HIS 0.005 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (17144) covalent geometry : angle 0.67000 / 0.36 (23653) hydrogen bonds : bond 0.04080 / 2.74 ( 775) hydrogen bonds : angle 5.74337 / 4.09 ( 2158) metal coordination : bond 0.03211 / 1.78 ( 8) metal coordination : angle 4.65484 / 2.68 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 0.545 Fit side-chains REVERT: A 529 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7304 (ttp-170) REVERT: A 531 ASP cc_start: 0.7678 (t0) cc_final: 0.7365 (t0) REVERT: A 731 ASP cc_start: 0.7814 (p0) cc_final: 0.7483 (p0) REVERT: A 743 PHE cc_start: 0.7803 (m-10) cc_final: 0.7528 (m-10) REVERT: A 877 GLU cc_start: 0.7815 (tp30) cc_final: 0.7564 (tp30) REVERT: A 929 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6358 (tm-30) REVERT: B 322 MET cc_start: 0.7791 (mtp) cc_final: 0.7569 (mtm) REVERT: B 344 TYR cc_start: 0.8555 (m-80) cc_final: 0.8321 (m-10) REVERT: C 524 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8223 (tttp) REVERT: C 691 MET cc_start: 0.8541 (mtp) cc_final: 0.8316 (mtm) REVERT: C 784 PHE cc_start: 0.8139 (t80) cc_final: 0.7687 (t80) REVERT: C 827 LYS cc_start: 0.8446 (tttt) cc_final: 0.7898 (tttm) REVERT: D 143 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7098 (m-30) REVERT: D 237 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7451 (ttm-80) REVERT: D 262 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8528 (mp) REVERT: D 264 THR cc_start: 0.8404 (t) cc_final: 0.8049 (t) REVERT: D 280 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6950 (tp30) REVERT: D 289 LEU cc_start: 0.8755 (tp) cc_final: 0.8466 (tm) REVERT: D 349 ARG cc_start: 0.7605 (mtp-110) cc_final: 0.7288 (mmt90) outliers start: 38 outliers final: 25 residues processed: 252 average time/residue: 0.5135 time to fit residues: 146.7943 Evaluate side-chains 227 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 262 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 174 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 0.0040 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 170 optimal weight: 0.2980 chunk 131 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN D 23 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.158963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.135790 restraints weight = 20137.921| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.52 r_work: 0.3539 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17152 Z= 0.159 Angle : 0.662 10.916 23657 Z= 0.356 Chirality : 0.046 0.353 2584 Planarity : 0.005 0.058 2643 Dihedral : 22.188 174.305 3170 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 2.35 % Allowed : 27.29 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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 (0.20), residues: 1766 helix: 0.22 (0.21), residues: 578 sheet: -2.28 (0.26), residues: 310 loop : -1.02 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 703 TYR 0.027 0.002 TYR C 707 PHE 0.012 0.002 PHE B 30 TRP 0.012 0.002 TRP B 317 HIS 0.004 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (17144) covalent geometry : angle 0.66058 / 0.36 (23653) hydrogen bonds : bond 0.03962 / 2.65 ( 775) hydrogen bonds : angle 5.68573 / 4.05 ( 2158) metal coordination : bond 0.02458 / 1.36 ( 8) metal coordination : angle 3.72946 / 2.15 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5130.20 seconds wall clock time: 88 minutes 42.82 seconds (5322.82 seconds total)