Starting phenix.real_space_refine on Tue Nov 18 18:34:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xnx_22272/11_2025/6xnx_22272.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xnx_22272/11_2025/6xnx_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_22272/11_2025/6xnx_22272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xnx_22272/11_2025/6xnx_22272.map" model { file = "/net/cci-nas-00/data/ceres_data/6xnx_22272/11_2025/6xnx_22272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xnx_22272/11_2025/6xnx_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-2.0-5881/lib/python3.9/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: 4.02, per 1000 atoms: 0.24 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: 1.82 Conformation dependent library (CDL) restraints added in 807.1 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: 3.14 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: 4.48 Time building geometry restraints manager: 2.31 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=" O3' DA y 30 " pdb=" P DC y 31 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.29e+01 bond pdb=" N TRP D 317 " pdb=" CA TRP D 317 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.16e-02 7.43e+03 1.14e+01 bond pdb=" CA ALA B 211 " pdb=" CB ALA B 211 " ideal model delta sigma weight residual 1.525 1.484 0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" O3' DC x 57 " pdb=" P DC x 58 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.73e+00 ... (remaining 17139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 23278 2.54 - 5.09: 356 5.09 - 7.63: 16 7.63 - 10.17: 2 10.17 - 12.72: 1 Bond angle restraints: 23653 Sorted by residual: 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=" CA ASP A 792 " pdb=" C ASP A 792 " pdb=" O ASP A 792 " ideal model delta sigma weight residual 121.66 116.48 5.18 1.17e+00 7.31e-01 1.96e+01 angle pdb=" C4' DG y 35 " pdb=" O4' DG y 35 " pdb=" C1' DG y 35 " ideal model delta sigma weight residual 109.70 103.10 6.60 1.50e+00 4.44e-01 1.94e+01 angle pdb=" C4' DG x 46 " pdb=" O4' DG x 46 " pdb=" C1' DG x 46 " ideal model delta sigma weight residual 109.70 103.26 6.44 1.50e+00 4.44e-01 1.84e+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 - 0.077: 2117 0.077 - 0.155: 435 0.155 - 0.232: 25 0.232 - 0.310: 1 0.310 - 0.387: 6 Chirality restraints: 2584 Sorted by residual: 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 chirality pdb=" CA ASP A 834 " pdb=" N ASP A 834 " pdb=" C ASP A 834 " pdb=" CB ASP A 834 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.35 2.00e-01 2.50e+01 3.15e+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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 23.920 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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= 0.561 Angle : 0.954 48.066 23657 Z= 0.477 Chirality : 0.060 0.387 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 covalent geometry : bond 0.01280 (17144) covalent geometry : angle 0.78968 (23653) hydrogen bonds : bond 0.13390 ( 775) hydrogen bonds : angle 8.15520 ( 2158) metal coordination : bond 0.13049 ( 8) metal coordination : angle 41.10463 ( 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 : 0.659 Fit side-chains revert: symmetry clash REVERT: A 743 PHE cc_start: 0.7846 (m-80) cc_final: 0.7334 (m-80) REVERT: A 827 LYS cc_start: 0.8199 (tptm) cc_final: 0.7996 (tttp) REVERT: A 861 GLU cc_start: 0.6737 (tt0) cc_final: 0.6514 (mm-30) REVERT: A 949 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7865 (ttp-170) REVERT: B 322 MET cc_start: 0.7600 (mtp) cc_final: 0.7343 (mtm) REVERT: C 571 GLU cc_start: 0.7697 (tt0) cc_final: 0.7441 (tt0) REVERT: C 627 MET cc_start: 0.9039 (mmm) cc_final: 0.8667 (mmm) REVERT: C 659 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8397 (mt) REVERT: C 691 MET cc_start: 0.8335 (mtp) cc_final: 0.7882 (mtm) REVERT: C 780 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.7986 (t) REVERT: C 848 MET cc_start: 0.7428 (ttp) cc_final: 0.7212 (ttp) REVERT: D 237 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7105 (ttm-80) REVERT: D 269 ASP cc_start: 0.7103 (m-30) cc_final: 0.6813 (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: 0.6943 time to fit residues: 253.2468 Evaluate side-chains 208 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 498 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 47 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 = 0.3881 r_free = 0.3881 target = 0.154655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131272 restraints weight = 19844.373| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.48 r_work: 0.3475 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 17152 Z= 0.210 Angle : 0.712 15.336 23657 Z= 0.377 Chirality : 0.045 0.173 2584 Planarity : 0.005 0.056 2643 Dihedral : 22.365 178.810 3191 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 4.45 % Allowed : 16.98 % Favored : 78.56 % 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: -2.70 (0.18), residues: 1766 helix: -0.75 (0.19), residues: 574 sheet: -3.10 (0.24), residues: 300 loop : -1.97 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 713 TYR 0.026 0.002 TYR A 725 PHE 0.015 0.002 PHE A 641 TRP 0.015 0.003 TRP B 307 HIS 0.011 0.002 HIS C 942 Details of bonding type rmsd covalent geometry : bond 0.00462 (17144) covalent geometry : angle 0.69142 (23653) hydrogen bonds : bond 0.04645 ( 775) hydrogen bonds : angle 6.34567 ( 2158) metal coordination : bond 0.06397 ( 8) metal coordination : angle 12.93423 ( 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 331 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 261 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 743 PHE cc_start: 0.8172 (m-80) cc_final: 0.7639 (m-80) REVERT: A 818 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.6621 (m-70) REVERT: A 824 GLU cc_start: 0.7494 (tp30) cc_final: 0.7049 (tp30) REVERT: A 861 GLU cc_start: 0.7279 (tt0) cc_final: 0.6798 (mm-30) REVERT: A 923 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7586 (mmtm) REVERT: B 49 ASP cc_start: 0.7945 (m-30) cc_final: 0.7603 (m-30) REVERT: B 286 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8340 (m) REVERT: B 322 MET cc_start: 0.7930 (mtp) cc_final: 0.7705 (mtm) REVERT: B 334 ASP cc_start: 0.5650 (t70) cc_final: 0.5187 (t0) REVERT: C 611 SER cc_start: 0.7516 (OUTLIER) cc_final: 0.7289 (p) REVERT: C 659 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8569 (mt) REVERT: C 691 MET cc_start: 0.8475 (mtp) cc_final: 0.7720 (mtm) REVERT: C 818 HIS cc_start: 0.6097 (m90) cc_final: 0.5861 (m170) REVERT: D 193 THR cc_start: 0.8485 (m) cc_final: 0.8178 (p) REVERT: D 237 ARG cc_start: 0.7549 (ttm110) cc_final: 0.7277 (ttm-80) REVERT: D 262 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8728 (mp) REVERT: D 316 ILE cc_start: 0.8488 (mp) cc_final: 0.8226 (mt) REVERT: D 349 ARG cc_start: 0.7635 (mtp-110) cc_final: 0.7300 (ttm110) outliers start: 70 outliers final: 19 residues processed: 307 average time/residue: 0.5953 time to fit residues: 205.4246 Evaluate side-chains 222 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 538 LEU 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 818 HIS 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 242 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain D residue 98 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 182 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS A 763 ASN ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 227 ASN C 473 ASN C1006 HIS D 16 GLN D 23 ASN D 27 GLN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.149146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124811 restraints weight = 20174.086| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.50 r_work: 0.3401 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2506 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= 0.280 Angle : 0.703 15.585 23657 Z= 0.373 Chirality : 0.046 0.178 2584 Planarity : 0.005 0.066 2643 Dihedral : 22.394 175.567 3174 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 4.96 % Allowed : 19.72 % Favored : 75.32 % 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: -2.19 (0.19), residues: 1766 helix: -0.33 (0.20), residues: 589 sheet: -2.96 (0.24), residues: 306 loop : -1.61 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 703 TYR 0.024 0.002 TYR A 725 PHE 0.021 0.002 PHE B 24 TRP 0.018 0.003 TRP B 317 HIS 0.009 0.002 HIS C 942 Details of bonding type rmsd covalent geometry : bond 0.00626 (17144) covalent geometry : angle 0.69051 (23653) hydrogen bonds : bond 0.05106 ( 775) hydrogen bonds : angle 6.19071 ( 2158) metal coordination : bond 0.06359 ( 8) metal coordination : angle 10.20568 ( 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 297 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 219 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7904 (t0) cc_final: 0.7666 (t0) REVERT: A 639 LYS cc_start: 0.8855 (ptpp) cc_final: 0.8580 (ptmt) REVERT: A 743 PHE cc_start: 0.8231 (m-80) cc_final: 0.7777 (m-80) REVERT: A 818 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.6840 (m-70) REVERT: A 824 GLU cc_start: 0.7680 (tp30) cc_final: 0.7327 (tp30) REVERT: B 49 ASP cc_start: 0.8004 (m-30) cc_final: 0.7691 (m-30) REVERT: B 143 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: B 219 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8727 (tt) REVERT: B 228 ILE cc_start: 0.8479 (pp) cc_final: 0.8195 (pp) REVERT: B 322 MET cc_start: 0.8060 (mtp) cc_final: 0.7784 (mtm) REVERT: C 627 MET cc_start: 0.9035 (mmm) cc_final: 0.8807 (mmm) REVERT: C 659 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8865 (mt) REVERT: C 682 MET cc_start: 0.8854 (mtp) cc_final: 0.8451 (mtm) REVERT: C 686 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: C 843 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8353 (pp) REVERT: D 5 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8012 (ttt) REVERT: D 237 ARG cc_start: 0.7738 (ttm110) cc_final: 0.7441 (ttm-80) REVERT: D 262 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8770 (mp) REVERT: D 289 LEU cc_start: 0.8895 (tp) cc_final: 0.8621 (tm) REVERT: D 298 GLU cc_start: 0.7596 (mp0) cc_final: 0.7342 (mp0) outliers start: 78 outliers final: 26 residues processed: 274 average time/residue: 0.5853 time to fit residues: 180.4088 Evaluate side-chains 232 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 642 GLU 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 98 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain D residue 5 MET 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: 0.8980 chunk 6 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 161 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 633 HIS B 54 HIS B 227 ASN C 818 HIS D 27 GLN ** D 47 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 = 0.3897 r_free = 0.3897 target = 0.155565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132163 restraints weight = 19810.300| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.49 r_work: 0.3498 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 17152 Z= 0.182 Angle : 0.656 11.370 23657 Z= 0.349 Chirality : 0.043 0.162 2584 Planarity : 0.005 0.069 2643 Dihedral : 22.269 178.799 3174 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 4.77 % Allowed : 21.12 % Favored : 74.11 % 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: -1.78 (0.19), residues: 1766 helix: -0.01 (0.21), residues: 580 sheet: -2.83 (0.23), residues: 314 loop : -1.26 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 529 TYR 0.023 0.002 TYR C 725 PHE 0.022 0.002 PHE B 24 TRP 0.013 0.002 TRP B 307 HIS 0.005 0.001 HIS C 942 Details of bonding type rmsd covalent geometry : bond 0.00402 (17144) covalent geometry : angle 0.65136 (23653) hydrogen bonds : bond 0.04065 ( 775) hydrogen bonds : angle 5.96012 ( 2158) metal coordination : bond 0.04350 ( 8) metal coordination : angle 6.03025 ( 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 306 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 231 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 529 ARG cc_start: 0.7603 (mtp180) cc_final: 0.7401 (ttp-170) REVERT: A 531 ASP cc_start: 0.7851 (t0) cc_final: 0.7582 (t0) REVERT: A 731 ASP cc_start: 0.7891 (p0) cc_final: 0.7524 (p0) REVERT: A 743 PHE cc_start: 0.8133 (m-80) cc_final: 0.7755 (m-80) REVERT: A 747 THR cc_start: 0.8434 (m) cc_final: 0.8227 (p) REVERT: A 818 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.6729 (m-70) REVERT: A 923 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7244 (mtpp) REVERT: B 49 ASP cc_start: 0.7892 (m-30) cc_final: 0.7422 (m-30) REVERT: B 143 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: B 228 ILE cc_start: 0.8467 (pp) cc_final: 0.8242 (pp) REVERT: B 300 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8071 (p) REVERT: C 627 MET cc_start: 0.8973 (mmm) cc_final: 0.8714 (mmm) REVERT: C 686 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: C 691 MET cc_start: 0.8386 (mtp) cc_final: 0.7802 (mtm) REVERT: C 827 LYS cc_start: 0.8460 (tttt) cc_final: 0.7920 (tttm) REVERT: C 843 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8207 (pp) REVERT: D 5 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7876 (ttt) REVERT: D 193 THR cc_start: 0.8555 (m) cc_final: 0.8232 (p) REVERT: D 237 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7443 (ttm-80) REVERT: D 262 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8633 (mp) outliers start: 75 outliers final: 25 residues processed: 288 average time/residue: 0.5593 time to fit residues: 181.6742 Evaluate side-chains 232 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 688 THR 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 143 ASP 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 300 SER 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 686 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 174 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: 3.9990 chunk 49 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.150274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126100 restraints weight = 20074.188| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.50 r_work: 0.3418 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 17152 Z= 0.269 Angle : 0.688 11.664 23657 Z= 0.365 Chirality : 0.045 0.180 2584 Planarity : 0.005 0.058 2643 Dihedral : 22.285 177.769 3171 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Rotamer: Outliers : 4.77 % Allowed : 21.69 % 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: -1.65 (0.19), residues: 1766 helix: 0.05 (0.21), residues: 582 sheet: -2.76 (0.24), residues: 311 loop : -1.16 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 349 TYR 0.025 0.002 TYR C 725 PHE 0.017 0.002 PHE B 24 TRP 0.014 0.002 TRP B 317 HIS 0.018 0.002 HIS C 818 Details of bonding type rmsd covalent geometry : bond 0.00607 (17144) covalent geometry : angle 0.68262 (23653) hydrogen bonds : bond 0.04707 ( 775) hydrogen bonds : angle 5.97840 ( 2158) metal coordination : bond 0.05286 ( 8) metal coordination : angle 6.70426 ( 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 280 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 205 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7963 (t0) cc_final: 0.7633 (t0) REVERT: A 731 ASP cc_start: 0.8076 (p0) cc_final: 0.7700 (p0) REVERT: A 743 PHE cc_start: 0.8158 (m-80) cc_final: 0.7779 (m-80) REVERT: A 747 THR cc_start: 0.8521 (m) cc_final: 0.8292 (p) REVERT: A 818 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.6825 (m-70) REVERT: A 923 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7547 (mtpp) REVERT: B 49 ASP cc_start: 0.7962 (m-30) cc_final: 0.7648 (m-30) REVERT: B 143 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: C 627 MET cc_start: 0.8999 (mmm) cc_final: 0.8777 (mmm) REVERT: C 659 LEU cc_start: 0.9267 (mt) cc_final: 0.8987 (mt) REVERT: C 686 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: C 827 LYS cc_start: 0.8469 (tttt) cc_final: 0.7898 (tttm) REVERT: D 5 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7943 (ttt) REVERT: D 237 ARG cc_start: 0.7805 (ttm110) cc_final: 0.7455 (ttm-80) REVERT: D 262 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8566 (mp) outliers start: 75 outliers final: 36 residues processed: 258 average time/residue: 0.5589 time to fit residues: 163.2753 Evaluate side-chains 232 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 735 LEU 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 143 ASP Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 233 LEU 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 300 SER 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 735 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 874 GLU Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain D residue 5 MET 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 174 SER Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 177 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 77 optimal weight: 0.0050 chunk 151 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.155446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131492 restraints weight = 19691.685| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.51 r_work: 0.3479 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 17152 Z= 0.174 Angle : 0.639 9.495 23657 Z= 0.343 Chirality : 0.043 0.267 2584 Planarity : 0.004 0.050 2643 Dihedral : 22.187 179.050 3170 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 4.45 % Allowed : 22.58 % Favored : 72.96 % 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: -1.57 (0.19), residues: 1766 helix: 0.15 (0.21), residues: 579 sheet: -2.65 (0.24), residues: 312 loop : -1.15 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 703 TYR 0.024 0.002 TYR C 725 PHE 0.020 0.002 PHE B 24 TRP 0.012 0.002 TRP B 307 HIS 0.005 0.001 HIS C 942 Details of bonding type rmsd covalent geometry : bond 0.00387 (17144) covalent geometry : angle 0.63618 (23653) hydrogen bonds : bond 0.03999 ( 775) hydrogen bonds : angle 5.84392 ( 2158) metal coordination : bond 0.03327 ( 8) metal coordination : angle 4.98814 ( 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 291 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 221 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7851 (t0) cc_final: 0.7538 (t0) REVERT: A 731 ASP cc_start: 0.8003 (p0) cc_final: 0.7656 (p0) REVERT: A 818 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.6741 (m-70) REVERT: B 49 ASP cc_start: 0.7852 (m-30) cc_final: 0.7382 (m-30) REVERT: B 143 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: B 289 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7574 (tm) REVERT: B 300 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8005 (p) REVERT: C 627 MET cc_start: 0.8952 (mmm) cc_final: 0.8689 (mmm) REVERT: C 686 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: C 827 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7869 (tttm) REVERT: D 5 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7490 (tpt) REVERT: D 143 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: D 237 ARG cc_start: 0.7741 (ttm110) cc_final: 0.7391 (ttm-80) REVERT: D 262 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8477 (mp) REVERT: D 280 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7143 (tp30) outliers start: 70 outliers final: 23 residues processed: 270 average time/residue: 0.5412 time to fit residues: 165.1672 Evaluate side-chains 219 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 642 GLU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 907 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 143 ASP 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 289 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 300 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 735 LEU Chi-restraints excluded: chain C residue 827 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain D residue 5 MET 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 143 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 818 HIS D 23 ASN ** D 47 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 = 0.3888 r_free = 0.3888 target = 0.155208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131681 restraints weight = 20090.545| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.49 r_work: 0.3482 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3428 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= 0.182 Angle : 0.648 10.153 23657 Z= 0.344 Chirality : 0.043 0.219 2584 Planarity : 0.005 0.065 2643 Dihedral : 22.132 179.112 3170 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 4.26 % Allowed : 23.28 % 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: -1.43 (0.19), residues: 1766 helix: 0.26 (0.21), residues: 579 sheet: -2.54 (0.25), residues: 312 loop : -1.07 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 529 TYR 0.024 0.002 TYR C 725 PHE 0.017 0.002 PHE B 24 TRP 0.011 0.002 TRP B 307 HIS 0.007 0.001 HIS C 818 Details of bonding type rmsd covalent geometry : bond 0.00411 (17144) covalent geometry : angle 0.64450 (23653) hydrogen bonds : bond 0.03994 ( 775) hydrogen bonds : angle 5.77412 ( 2158) metal coordination : bond 0.03416 ( 8) metal coordination : angle 5.07694 ( 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: 67 poor density : 212 time to evaluate : 0.629 Fit side-chains REVERT: A 531 ASP cc_start: 0.7841 (t0) cc_final: 0.7508 (t0) REVERT: A 731 ASP cc_start: 0.7934 (p0) cc_final: 0.7634 (p0) REVERT: A 743 PHE cc_start: 0.7962 (m-10) cc_final: 0.7732 (m-10) REVERT: A 818 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.6820 (m-70) REVERT: A 877 GLU cc_start: 0.7809 (tp30) cc_final: 0.7587 (tp30) REVERT: A 923 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7317 (mtpp) REVERT: B 49 ASP cc_start: 0.7706 (m-30) cc_final: 0.7422 (m-30) REVERT: B 143 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7473 (m-30) REVERT: B 289 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7472 (tm) REVERT: B 300 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.7990 (p) REVERT: C 529 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7391 (ttp-170) REVERT: C 627 MET cc_start: 0.8959 (mmm) cc_final: 0.8714 (mmm) REVERT: C 827 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7979 (tttm) REVERT: D 5 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7405 (tpt) REVERT: D 143 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7047 (m-30) REVERT: D 227 ASN cc_start: 0.7939 (t0) cc_final: 0.7736 (t0) REVERT: D 237 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7387 (ttm-80) REVERT: D 262 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8473 (mp) REVERT: D 280 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7086 (tp30) REVERT: D 298 GLU cc_start: 0.7414 (mp0) cc_final: 0.7009 (mp0) outliers start: 67 outliers final: 30 residues processed: 260 average time/residue: 0.5611 time to fit residues: 165.1662 Evaluate side-chains 231 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 688 THR 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 143 ASP 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 289 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 827 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 874 GLU Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 5 MET 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 174 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.8980 chunk 93 optimal weight: 0.0770 chunk 124 optimal weight: 3.9990 chunk 7 optimal weight: 0.0980 chunk 6 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 111 optimal weight: 0.0170 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.158568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135170 restraints weight = 20030.332| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.51 r_work: 0.3553 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17152 Z= 0.159 Angle : 0.633 9.034 23657 Z= 0.339 Chirality : 0.043 0.161 2584 Planarity : 0.005 0.050 2643 Dihedral : 22.037 179.963 3170 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 3.24 % Allowed : 24.49 % Favored : 72.26 % 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: -1.31 (0.20), residues: 1766 helix: 0.34 (0.21), residues: 579 sheet: -2.34 (0.26), residues: 304 loop : -1.06 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 529 TYR 0.023 0.002 TYR C 725 PHE 0.019 0.002 PHE B 24 TRP 0.017 0.002 TRP B 307 HIS 0.020 0.001 HIS C 818 Details of bonding type rmsd covalent geometry : bond 0.00356 (17144) covalent geometry : angle 0.62975 (23653) hydrogen bonds : bond 0.03749 ( 775) hydrogen bonds : angle 5.65212 ( 2158) metal coordination : bond 0.02539 ( 8) metal coordination : angle 4.63053 ( 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: 51 poor density : 227 time to evaluate : 0.603 Fit side-chains REVERT: A 531 ASP cc_start: 0.7702 (t0) cc_final: 0.7415 (t0) REVERT: A 731 ASP cc_start: 0.7741 (p0) cc_final: 0.7420 (p0) REVERT: A 743 PHE cc_start: 0.7825 (m-10) cc_final: 0.7538 (m-10) REVERT: A 877 GLU cc_start: 0.7757 (tp30) cc_final: 0.7541 (tp30) REVERT: A 929 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6330 (tm-30) REVERT: B 143 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: B 289 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7226 (tm) REVERT: B 300 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7953 (p) REVERT: C 524 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8252 (tptt) REVERT: C 529 ARG cc_start: 0.7690 (mtp-110) cc_final: 0.7267 (ttp-170) REVERT: C 627 MET cc_start: 0.8931 (mmm) cc_final: 0.8711 (mmm) REVERT: C 827 LYS cc_start: 0.8433 (tttt) cc_final: 0.7999 (tttm) REVERT: D 142 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8419 (tt) REVERT: D 143 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: D 237 ARG cc_start: 0.7730 (ttm110) cc_final: 0.7459 (ttm-80) REVERT: D 262 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8459 (mp) REVERT: D 280 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7044 (tp30) REVERT: D 298 GLU cc_start: 0.7348 (mp0) cc_final: 0.6963 (mp0) REVERT: D 349 ARG cc_start: 0.7658 (mtp-110) cc_final: 0.7244 (mmt90) outliers start: 51 outliers final: 23 residues processed: 269 average time/residue: 0.5303 time to fit residues: 161.8311 Evaluate side-chains 225 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 688 THR Chi-restraints excluded: chain A residue 936 PHE 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 143 ASP Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 874 GLU 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 133 VAL Chi-restraints excluded: chain D residue 142 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.158697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.135421 restraints weight = 19994.446| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.51 r_work: 0.3555 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17152 Z= 0.165 Angle : 0.638 8.954 23657 Z= 0.340 Chirality : 0.043 0.188 2584 Planarity : 0.005 0.105 2643 Dihedral : 22.015 179.751 3170 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 2.74 % Allowed : 25.83 % Favored : 71.44 % 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: -1.23 (0.20), residues: 1766 helix: 0.34 (0.21), residues: 579 sheet: -2.27 (0.27), residues: 285 loop : -1.02 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 529 TYR 0.025 0.002 TYR A 514 PHE 0.024 0.002 PHE B 24 TRP 0.012 0.002 TRP B 307 HIS 0.004 0.001 HIS C 942 Details of bonding type rmsd covalent geometry : bond 0.00372 (17144) covalent geometry : angle 0.63531 (23653) hydrogen bonds : bond 0.03842 ( 775) hydrogen bonds : angle 5.61514 ( 2158) metal coordination : bond 0.02708 ( 8) metal coordination : angle 4.60251 ( 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 263 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.595 Fit side-chains REVERT: A 531 ASP cc_start: 0.7656 (t0) cc_final: 0.7379 (t0) REVERT: A 731 ASP cc_start: 0.7735 (p0) cc_final: 0.7410 (p0) REVERT: A 743 PHE cc_start: 0.7777 (m-10) cc_final: 0.7504 (m-10) REVERT: A 877 GLU cc_start: 0.7807 (tp30) cc_final: 0.7523 (tp30) REVERT: A 929 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6227 (tm-30) REVERT: B 49 ASP cc_start: 0.7398 (m-30) cc_final: 0.7129 (m-30) REVERT: B 143 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: C 529 ARG cc_start: 0.7680 (mtp-110) cc_final: 0.7208 (ttp-170) REVERT: C 617 GLU cc_start: 0.7895 (mm-30) cc_final: 0.6982 (tt0) REVERT: C 627 MET cc_start: 0.8945 (mmm) cc_final: 0.8738 (mmm) REVERT: C 743 PHE cc_start: 0.8543 (m-80) cc_final: 0.8272 (m-80) REVERT: C 827 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8019 (tttm) REVERT: D 142 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8428 (tt) REVERT: D 143 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: D 237 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7463 (ttm-80) REVERT: D 262 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8474 (mp) REVERT: D 280 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7002 (tp30) REVERT: D 298 GLU cc_start: 0.7364 (mp0) cc_final: 0.6985 (mp0) REVERT: D 349 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7219 (mmt90) outliers start: 43 outliers final: 25 residues processed: 253 average time/residue: 0.5716 time to fit residues: 163.2514 Evaluate side-chains 237 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 664 ASP Chi-restraints excluded: chain A residue 688 THR 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 143 ASP Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 827 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 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 142 ILE 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: 3.9990 chunk 155 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 HIS D 23 ASN ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133240 restraints weight = 19930.058| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.52 r_work: 0.3526 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17152 Z= 0.194 Angle : 0.654 9.948 23657 Z= 0.346 Chirality : 0.043 0.175 2584 Planarity : 0.005 0.049 2643 Dihedral : 22.038 179.559 3170 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 3.05 % Allowed : 26.53 % Favored : 70.42 % 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: -1.21 (0.20), residues: 1766 helix: 0.33 (0.21), residues: 580 sheet: -2.24 (0.28), residues: 285 loop : -0.99 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 529 TYR 0.025 0.002 TYR A 514 PHE 0.020 0.002 PHE B 24 TRP 0.010 0.002 TRP C 829 HIS 0.007 0.001 HIS C 818 Details of bonding type rmsd covalent geometry : bond 0.00440 (17144) covalent geometry : angle 0.65116 (23653) hydrogen bonds : bond 0.04008 ( 775) hydrogen bonds : angle 5.62063 ( 2158) metal coordination : bond 0.03153 ( 8) metal coordination : angle 5.02457 ( 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 254 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.654 Fit side-chains REVERT: A 531 ASP cc_start: 0.7710 (t0) cc_final: 0.7424 (t0) REVERT: A 639 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7967 (ttmt) REVERT: A 664 ASP cc_start: 0.8522 (t0) cc_final: 0.8294 (t70) REVERT: A 690 GLU cc_start: 0.8196 (tt0) cc_final: 0.7638 (mp0) REVERT: A 731 ASP cc_start: 0.7761 (p0) cc_final: 0.7444 (p0) REVERT: A 743 PHE cc_start: 0.7757 (m-10) cc_final: 0.7521 (m-10) REVERT: A 828 ARG cc_start: 0.7974 (mmp80) cc_final: 0.7698 (ttm-80) REVERT: A 877 GLU cc_start: 0.7823 (tp30) cc_final: 0.7543 (tp30) REVERT: A 929 GLU cc_start: 0.6656 (tm-30) cc_final: 0.6453 (tm-30) REVERT: B 49 ASP cc_start: 0.7419 (m-30) cc_final: 0.7054 (m-30) REVERT: B 143 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: C 529 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.7191 (ttp-170) REVERT: C 627 MET cc_start: 0.8950 (mmm) cc_final: 0.8735 (mmm) REVERT: C 743 PHE cc_start: 0.8558 (m-80) cc_final: 0.8313 (m-80) REVERT: C 827 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8041 (tttm) REVERT: D 142 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8425 (tt) REVERT: D 143 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: D 237 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7482 (ttm-80) REVERT: D 242 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6337 (tm) REVERT: D 262 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8522 (mp) REVERT: D 280 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6998 (tp30) REVERT: D 298 GLU cc_start: 0.7381 (mp0) cc_final: 0.7000 (mp0) outliers start: 48 outliers final: 32 residues processed: 241 average time/residue: 0.5455 time to fit residues: 149.5482 Evaluate side-chains 232 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 639 LYS Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 658 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 827 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 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 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 242 LEU 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: 0.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 131 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS C 818 HIS ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134555 restraints weight = 19724.693| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.51 r_work: 0.3528 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17152 Z= 0.185 Angle : 0.657 10.663 23657 Z= 0.347 Chirality : 0.043 0.170 2584 Planarity : 0.004 0.048 2643 Dihedral : 22.031 179.236 3170 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 2.93 % Allowed : 26.91 % Favored : 70.17 % 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: -1.24 (0.20), residues: 1766 helix: 0.30 (0.21), residues: 580 sheet: -2.25 (0.26), residues: 305 loop : -0.96 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 349 TYR 0.024 0.002 TYR A 514 PHE 0.020 0.002 PHE B 24 TRP 0.012 0.002 TRP C 829 HIS 0.005 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00419 (17144) covalent geometry : angle 0.65410 (23653) hydrogen bonds : bond 0.03955 ( 775) hydrogen bonds : angle 5.62627 ( 2158) metal coordination : bond 0.02858 ( 8) metal coordination : angle 4.75839 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6019.59 seconds wall clock time: 103 minutes 43.88 seconds (6223.88 seconds total)