Starting phenix.real_space_refine on Wed Mar 4 20:55:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xnx_22272/03_2026/6xnx_22272.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xnx_22272/03_2026/6xnx_22272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xnx_22272/03_2026/6xnx_22272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xnx_22272/03_2026/6xnx_22272.map" model { file = "/net/cci-nas-00/data/ceres_data/6xnx_22272/03_2026/6xnx_22272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xnx_22272/03_2026/6xnx_22272.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 110 5.49 5 Mg 4 5.21 5 S 106 5.16 5 C 10116 2.51 5 N 2888 2.21 5 O 3314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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: 3.67, per 1000 atoms: 0.22 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: 1.53 Conformation dependent library (CDL) restraints added in 683.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1103 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 727 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " Number of angles added : 4 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 20 sheets defined 35.9% alpha, 22.3% beta 54 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 492 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.903A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 824 through 840 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.675A pdb=" N GLU A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 895 Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 953 through 957 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.645A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 996 through 1003 removed outlier: 3.606A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.803A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 492 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.689A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 581 removed outlier: 4.873A pdb=" N GLU C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP C 573 " --> pdb=" O ASP C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 684 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 Processing helix chain 'C' and resid 822 through 840 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 908 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 958 through 975 Processing helix chain 'C' and resid 979 through 995 removed outlier: 4.805A pdb=" N MET C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 519 removed outlier: 4.854A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519 removed outlier: 4.854A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.719A pdb=" N PHE B 24 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 8 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N PHE B 343 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.150A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.014A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AB1, first strand: chain 'C' and resid 517 through 519 removed outlier: 6.538A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 517 through 519 removed outlier: 6.538A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 631 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS C 639 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS C 633 " --> pdb=" O ASN C 637 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN C 637 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.431A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 22 through 24 removed outlier: 4.795A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.160A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG D 123 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL D 112 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR D 125 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N MET D 110 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS D 127 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR D 108 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.351A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.791A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 267 removed outlier: 6.882A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 277 through 279 682 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 274 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 2.01 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: 1.390 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.010 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- 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 : 0.588 Fit side-chains revert: symmetry clash REVERT: A 743 PHE cc_start: 0.7846 (m-80) cc_final: 0.7333 (m-80) REVERT: A 827 LYS cc_start: 0.8196 (tptm) cc_final: 0.7994 (tttp) REVERT: A 861 GLU cc_start: 0.6735 (tt0) cc_final: 0.6513 (mm-30) REVERT: A 949 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7866 (ttp-170) REVERT: B 322 MET cc_start: 0.7599 (mtp) cc_final: 0.7341 (mtm) REVERT: C 571 GLU cc_start: 0.7693 (tt0) cc_final: 0.7440 (tt0) REVERT: C 627 MET cc_start: 0.9041 (mmm) cc_final: 0.8667 (mmm) REVERT: C 659 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8395 (mt) REVERT: C 691 MET cc_start: 0.8335 (mtp) cc_final: 0.7884 (mtm) REVERT: C 701 ILE cc_start: 0.9102 (mt) cc_final: 0.8902 (mm) REVERT: C 780 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.7987 (t) REVERT: C 848 MET cc_start: 0.7431 (ttp) cc_final: 0.7209 (ttp) REVERT: D 237 ARG cc_start: 0.7410 (ttm110) cc_final: 0.7106 (ttm-80) REVERT: D 269 ASP cc_start: 0.7100 (m-30) cc_final: 0.6811 (m-30) REVERT: D 316 ILE cc_start: 0.8332 (mp) cc_final: 0.8100 (mt) outliers start: 37 outliers final: 19 residues processed: 330 average time/residue: 0.6598 time to fit residues: 240.8278 Evaluate side-chains 209 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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** D 117 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.153336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129809 restraints weight = 19884.597| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.47 r_work: 0.3467 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 17152 Z= 0.221 Angle : 0.712 16.815 23657 Z= 0.375 Chirality : 0.044 0.168 2584 Planarity : 0.005 0.057 2643 Dihedral : 22.355 178.037 3191 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 4.26 % Allowed : 17.18 % 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: -2.80 (0.18), residues: 1766 helix: -0.82 (0.19), residues: 576 sheet: -3.14 (0.23), residues: 312 loop : -2.04 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 713 TYR 0.023 0.002 TYR A 725 PHE 0.017 0.002 PHE D 29 TRP 0.015 0.002 TRP B 317 HIS 0.011 0.002 HIS C 942 Details of bonding type rmsd covalent geometry : bond 0.00486 (17144) covalent geometry : angle 0.68651 (23653) hydrogen bonds : bond 0.04919 ( 775) hydrogen bonds : angle 6.40276 ( 2158) metal coordination : bond 0.06660 ( 8) metal coordination : angle 14.46669 ( 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 321 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 254 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 743 PHE cc_start: 0.8170 (m-80) cc_final: 0.7644 (m-80) REVERT: A 763 ASN cc_start: 0.8285 (t0) cc_final: 0.8081 (t0) REVERT: A 818 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.6637 (m-70) REVERT: A 824 GLU cc_start: 0.7491 (tp30) cc_final: 0.7045 (tp30) REVERT: A 861 GLU cc_start: 0.7296 (tt0) cc_final: 0.6815 (mm-30) REVERT: A 923 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7620 (mmtm) REVERT: B 49 ASP cc_start: 0.7964 (m-30) cc_final: 0.7620 (m-30) REVERT: B 188 GLU cc_start: 0.6898 (mp0) cc_final: 0.6693 (mp0) REVERT: B 286 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8325 (m) REVERT: B 289 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8260 (tm) REVERT: B 300 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8062 (p) REVERT: B 322 MET cc_start: 0.7921 (mtp) cc_final: 0.7697 (mtm) REVERT: B 334 ASP cc_start: 0.5708 (t70) cc_final: 0.5204 (t0) REVERT: B 349 ARG cc_start: 0.7726 (ttp-110) cc_final: 0.7236 (ttp80) REVERT: C 611 SER cc_start: 0.7508 (OUTLIER) cc_final: 0.7280 (p) REVERT: C 627 MET cc_start: 0.9111 (mmm) cc_final: 0.8908 (mmm) REVERT: C 659 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8745 (mt) REVERT: C 691 MET cc_start: 0.8482 (mtp) cc_final: 0.7787 (mtm) REVERT: C 818 HIS cc_start: 0.6125 (m90) cc_final: 0.5884 (m170) REVERT: D 193 THR cc_start: 0.8551 (m) cc_final: 0.8228 (p) REVERT: D 237 ARG cc_start: 0.7555 (ttm110) cc_final: 0.7275 (ttm-80) REVERT: D 262 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8733 (mp) REVERT: D 349 ARG cc_start: 0.7649 (mtp-110) cc_final: 0.7291 (ttm110) outliers start: 67 outliers final: 16 residues processed: 299 average time/residue: 0.5791 time to fit residues: 194.4748 Evaluate side-chains 216 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 286 VAL 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 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 347 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 182 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.131333 restraints weight = 20269.172| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.48 r_work: 0.3488 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 17152 Z= 0.195 Angle : 0.655 12.714 23657 Z= 0.351 Chirality : 0.043 0.197 2584 Planarity : 0.005 0.077 2643 Dihedral : 22.243 176.942 3174 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 4.64 % Allowed : 19.91 % Favored : 75.45 % 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: -2.16 (0.19), residues: 1766 helix: -0.22 (0.20), residues: 582 sheet: -2.98 (0.23), residues: 327 loop : -1.56 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 703 TYR 0.022 0.002 TYR C 805 PHE 0.021 0.002 PHE B 24 TRP 0.015 0.002 TRP B 307 HIS 0.008 0.001 HIS C 942 Details of bonding type rmsd covalent geometry : bond 0.00432 (17144) covalent geometry : angle 0.64451 (23653) hydrogen bonds : bond 0.04343 ( 775) hydrogen bonds : angle 6.07072 ( 2158) metal coordination : bond 0.05470 ( 8) metal coordination : angle 9.09465 ( 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 312 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 239 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7761 (t0) cc_final: 0.7554 (t0) REVERT: A 664 ASP cc_start: 0.8383 (t0) cc_final: 0.8170 (t0) REVERT: A 743 PHE cc_start: 0.8158 (m-80) cc_final: 0.7675 (m-80) REVERT: A 747 THR cc_start: 0.8560 (m) cc_final: 0.8317 (p) REVERT: A 818 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.6676 (m-70) REVERT: A 824 GLU cc_start: 0.7548 (tp30) cc_final: 0.7278 (tp30) REVERT: A 861 GLU cc_start: 0.7283 (tt0) cc_final: 0.6775 (mm-30) REVERT: A 923 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7432 (mmtp) REVERT: B 49 ASP cc_start: 0.7912 (m-30) cc_final: 0.7552 (m-30) REVERT: B 77 THR cc_start: 0.8258 (t) cc_final: 0.8008 (p) REVERT: B 228 ILE cc_start: 0.8420 (pp) cc_final: 0.8147 (pp) REVERT: B 289 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8332 (tm) REVERT: B 322 MET cc_start: 0.7941 (mtp) cc_final: 0.7713 (mtm) REVERT: C 547 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7722 (mm-30) REVERT: C 659 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8878 (mt) REVERT: C 686 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: C 691 MET cc_start: 0.8296 (mtp) cc_final: 0.7746 (mtm) REVERT: C 784 PHE cc_start: 0.8113 (t80) cc_final: 0.7837 (t80) REVERT: C 839 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8239 (mtpp) REVERT: D 105 ASP cc_start: 0.7211 (p0) cc_final: 0.6872 (p0) REVERT: D 179 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8219 (mp) REVERT: D 193 THR cc_start: 0.8507 (m) cc_final: 0.8182 (p) REVERT: D 237 ARG cc_start: 0.7545 (ttm110) cc_final: 0.7272 (ttm-80) REVERT: D 289 LEU cc_start: 0.8905 (tp) cc_final: 0.8645 (tm) outliers start: 73 outliers final: 22 residues processed: 289 average time/residue: 0.5472 time to fit residues: 178.5840 Evaluate side-chains 226 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 226 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 LEU 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 859 THR Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 260 SER 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: 0.9980 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 ASN A 990 HIS B 54 HIS C 818 HIS D 27 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.147282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122492 restraints weight = 19593.140| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.52 r_work: 0.3365 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.146 17152 Z= 0.336 Angle : 0.738 15.458 23657 Z= 0.390 Chirality : 0.047 0.189 2584 Planarity : 0.005 0.077 2643 Dihedral : 22.452 176.620 3173 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.17 % Rotamer: Outliers : 5.92 % Allowed : 19.72 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.19), residues: 1766 helix: -0.23 (0.20), residues: 590 sheet: -2.87 (0.24), residues: 293 loop : -1.42 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 529 TYR 0.025 0.003 TYR C 725 PHE 0.019 0.002 PHE D 206 TRP 0.021 0.003 TRP B 317 HIS 0.008 0.002 HIS C 836 Details of bonding type rmsd covalent geometry : bond 0.00756 (17144) covalent geometry : angle 0.72831 (23653) hydrogen bonds : bond 0.05467 ( 775) hydrogen bonds : angle 6.18805 ( 2158) metal coordination : bond 0.07120 ( 8) metal coordination : angle 9.42788 ( 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 305 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 212 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 731 ASP cc_start: 0.8096 (p0) cc_final: 0.7783 (p0) REVERT: A 743 PHE cc_start: 0.8209 (m-80) cc_final: 0.7764 (m-80) REVERT: A 818 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.6805 (m-70) REVERT: A 824 GLU cc_start: 0.7696 (tp30) cc_final: 0.7474 (tp30) REVERT: A 923 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7621 (mtpp) REVERT: A 970 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8742 (ttt-90) REVERT: B 49 ASP cc_start: 0.8002 (m-30) cc_final: 0.7635 (m-30) REVERT: B 219 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8699 (tt) REVERT: B 289 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8462 (tm) REVERT: B 298 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: B 322 MET cc_start: 0.8176 (mtp) cc_final: 0.7911 (mtm) REVERT: C 682 MET cc_start: 0.8903 (mtp) cc_final: 0.8565 (mtm) REVERT: C 691 MET cc_start: 0.8534 (mtp) cc_final: 0.8051 (mtm) REVERT: D 5 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7953 (ttt) REVERT: D 237 ARG cc_start: 0.7886 (ttm110) cc_final: 0.7604 (ttm-80) REVERT: D 262 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8506 (mp) REVERT: D 289 LEU cc_start: 0.8951 (tp) cc_final: 0.8683 (tm) outliers start: 93 outliers final: 37 residues processed: 279 average time/residue: 0.5627 time to fit residues: 176.6265 Evaluate side-chains 229 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 658 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 726 ILE 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 A residue 970 ARG Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 LEU 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 298 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 768 SER Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 110 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 291 SER Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 340 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: 1.9990 chunk 49 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 830 GLN B 54 HIS C 818 HIS D 23 ASN D 27 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.152249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.128003 restraints weight = 19840.073| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.51 r_work: 0.3445 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 17152 Z= 0.203 Angle : 0.660 12.131 23657 Z= 0.353 Chirality : 0.043 0.165 2584 Planarity : 0.005 0.071 2643 Dihedral : 22.293 178.545 3171 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 5.28 % Allowed : 21.56 % Favored : 73.16 % 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: -1.71 (0.19), residues: 1766 helix: 0.01 (0.21), residues: 581 sheet: -2.74 (0.25), residues: 298 loop : -1.25 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 349 TYR 0.024 0.002 TYR C 725 PHE 0.013 0.002 PHE B 30 TRP 0.014 0.002 TRP B 307 HIS 0.021 0.002 HIS C 818 Details of bonding type rmsd covalent geometry : bond 0.00453 (17144) covalent geometry : angle 0.65462 (23653) hydrogen bonds : bond 0.04256 ( 775) hydrogen bonds : angle 6.01012 ( 2158) metal coordination : bond 0.04594 ( 8) metal coordination : angle 6.34132 ( 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 300 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 217 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7923 (t0) cc_final: 0.7622 (t0) REVERT: A 731 ASP cc_start: 0.8076 (p0) cc_final: 0.7803 (p0) REVERT: A 743 PHE cc_start: 0.8123 (m-80) cc_final: 0.7743 (m-80) REVERT: A 818 HIS cc_start: 0.7741 (OUTLIER) cc_final: 0.6774 (m-70) REVERT: A 923 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7439 (mtpp) REVERT: A 970 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8662 (ttt-90) REVERT: B 49 ASP cc_start: 0.7916 (m-30) cc_final: 0.7594 (m-30) REVERT: B 322 MET cc_start: 0.7955 (mtp) cc_final: 0.7715 (mtm) REVERT: C 529 ARG cc_start: 0.7425 (ttp-170) cc_final: 0.7168 (mtp-110) REVERT: C 627 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8650 (mmm) REVERT: C 659 LEU cc_start: 0.9143 (mt) cc_final: 0.8894 (mt) REVERT: C 686 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: C 691 MET cc_start: 0.8439 (mtp) cc_final: 0.7928 (mtm) REVERT: C 843 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8331 (pp) REVERT: C 974 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7819 (mtt) REVERT: D 5 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7529 (tpt) REVERT: D 179 LEU cc_start: 0.8618 (mp) cc_final: 0.8414 (mt) REVERT: D 202 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6649 (t70) REVERT: D 237 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7442 (ttm-80) REVERT: D 262 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8449 (mp) REVERT: D 289 LEU cc_start: 0.8917 (tp) cc_final: 0.8699 (tm) REVERT: D 298 GLU cc_start: 0.7538 (mp0) cc_final: 0.7314 (mp0) outliers start: 83 outliers final: 26 residues processed: 274 average time/residue: 0.5306 time to fit residues: 163.9520 Evaluate side-chains 226 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 771 GLU 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 A residue 970 ARG 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 205 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 627 MET 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 843 LEU 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 C residue 974 MET Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 177 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 151 optimal weight: 0.0980 chunk 85 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 647 ASN D 23 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.156281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132800 restraints weight = 20075.564| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.50 r_work: 0.3487 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3287 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= 0.172 Angle : 0.645 9.821 23657 Z= 0.344 Chirality : 0.043 0.276 2584 Planarity : 0.005 0.059 2643 Dihedral : 22.175 178.906 3170 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 4.13 % Allowed : 22.96 % Favored : 72.90 % 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: -1.54 (0.19), residues: 1766 helix: 0.11 (0.21), residues: 580 sheet: -2.65 (0.25), residues: 298 loop : -1.12 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 703 TYR 0.023 0.002 TYR C 725 PHE 0.012 0.002 PHE B 30 TRP 0.014 0.002 TRP B 307 HIS 0.005 0.001 HIS C 942 Details of bonding type rmsd covalent geometry : bond 0.00382 (17144) covalent geometry : angle 0.64157 (23653) hydrogen bonds : bond 0.04000 ( 775) hydrogen bonds : angle 5.84852 ( 2158) metal coordination : bond 0.03539 ( 8) metal coordination : angle 5.14124 ( 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 287 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 222 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7878 (t0) cc_final: 0.7539 (t0) REVERT: A 731 ASP cc_start: 0.7978 (p0) cc_final: 0.7650 (p0) REVERT: A 818 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.6762 (m-70) REVERT: A 923 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7344 (mtpp) REVERT: A 970 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8699 (ttt-90) REVERT: B 49 ASP cc_start: 0.7818 (m-30) cc_final: 0.7386 (m-30) REVERT: C 529 ARG cc_start: 0.7336 (ttp-170) cc_final: 0.7130 (mtp-110) REVERT: C 546 ASP cc_start: 0.8459 (m-30) cc_final: 0.8198 (m-30) REVERT: C 627 MET cc_start: 0.8925 (mmm) cc_final: 0.8724 (mmm) REVERT: C 691 MET cc_start: 0.8393 (mtp) cc_final: 0.7872 (mtm) REVERT: C 784 PHE cc_start: 0.8210 (t80) cc_final: 0.7774 (t80) REVERT: C 824 GLU cc_start: 0.7759 (pp20) cc_final: 0.7495 (pp20) REVERT: C 827 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7918 (tttm) REVERT: C 843 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8241 (pp) REVERT: C 974 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7776 (mtt) REVERT: D 5 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7482 (tpt) REVERT: D 143 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: D 202 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6622 (t70) REVERT: D 237 ARG cc_start: 0.7737 (ttm110) cc_final: 0.7379 (ttm-80) REVERT: D 262 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8453 (mp) REVERT: D 280 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7173 (tp30) REVERT: D 289 LEU cc_start: 0.8847 (tp) cc_final: 0.8635 (tm) REVERT: D 298 GLU cc_start: 0.7414 (mp0) cc_final: 0.7186 (mp0) outliers start: 65 outliers final: 20 residues processed: 266 average time/residue: 0.5370 time to fit residues: 161.7938 Evaluate side-chains 225 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 818 HIS Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain A residue 970 ARG 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 205 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 827 LYS Chi-restraints excluded: chain C residue 843 LEU 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 974 MET Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 4 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 8.9990 chunk 48 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 818 HIS D 23 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3922 r_free = 0.3922 target = 0.157547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134172 restraints weight = 19823.915| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.50 r_work: 0.3526 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17152 Z= 0.170 Angle : 0.640 9.384 23657 Z= 0.341 Chirality : 0.043 0.191 2584 Planarity : 0.004 0.049 2643 Dihedral : 22.093 179.357 3170 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.73 % Rotamer: Outliers : 3.88 % Allowed : 23.85 % 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: -1.40 (0.20), residues: 1766 helix: 0.26 (0.21), residues: 581 sheet: -2.47 (0.25), residues: 311 loop : -1.07 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 349 TYR 0.023 0.002 TYR C 725 PHE 0.014 0.002 PHE A 911 TRP 0.012 0.002 TRP B 307 HIS 0.006 0.001 HIS C 818 Details of bonding type rmsd covalent geometry : bond 0.00382 (17144) covalent geometry : angle 0.63733 (23653) hydrogen bonds : bond 0.03870 ( 775) hydrogen bonds : angle 5.72799 ( 2158) metal coordination : bond 0.03143 ( 8) metal coordination : angle 4.57902 ( 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 288 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 227 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7906 (ptt-90) cc_final: 0.7696 (ptt-90) REVERT: A 531 ASP cc_start: 0.7767 (t0) cc_final: 0.7485 (t0) REVERT: A 731 ASP cc_start: 0.7856 (p0) cc_final: 0.7604 (p0) REVERT: A 743 PHE cc_start: 0.7889 (m-10) cc_final: 0.7653 (m-10) REVERT: A 818 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.6782 (m-70) REVERT: A 828 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7539 (ttm-80) REVERT: A 877 GLU cc_start: 0.7802 (tp30) cc_final: 0.7594 (tp30) REVERT: A 970 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8618 (ttt-90) REVERT: B 49 ASP cc_start: 0.7593 (m-30) cc_final: 0.7352 (m-30) REVERT: C 784 PHE cc_start: 0.8181 (t80) cc_final: 0.7744 (t80) REVERT: C 827 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7951 (tttm) REVERT: C 843 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8276 (pp) REVERT: C 974 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7677 (mtt) REVERT: D 5 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7310 (tpt) REVERT: D 143 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: D 227 ASN cc_start: 0.7913 (t0) cc_final: 0.7703 (t0) REVERT: D 237 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7398 (ttm-80) REVERT: D 262 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8463 (mp) REVERT: D 280 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7113 (tp30) REVERT: D 289 LEU cc_start: 0.8772 (tp) cc_final: 0.8481 (tm) outliers start: 61 outliers final: 23 residues processed: 265 average time/residue: 0.5607 time to fit residues: 167.3477 Evaluate side-chains 225 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 726 ILE Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 970 ARG Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 827 LYS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 4.9990 chunk 93 optimal weight: 0.1980 chunk 124 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 166 GLN C 818 HIS D 23 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.157246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133634 restraints weight = 19882.358| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.50 r_work: 0.3516 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17152 Z= 0.181 Angle : 0.647 9.084 23657 Z= 0.345 Chirality : 0.043 0.199 2584 Planarity : 0.005 0.057 2643 Dihedral : 22.072 179.664 3170 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 3.63 % Allowed : 24.81 % Favored : 71.56 % 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: -1.28 (0.20), residues: 1766 helix: 0.32 (0.21), residues: 580 sheet: -2.35 (0.27), residues: 286 loop : -1.04 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 529 TYR 0.023 0.002 TYR C 725 PHE 0.014 0.001 PHE B 48 TRP 0.014 0.002 TRP B 307 HIS 0.017 0.001 HIS C 818 Details of bonding type rmsd covalent geometry : bond 0.00409 (17144) covalent geometry : angle 0.64449 (23653) hydrogen bonds : bond 0.03946 ( 775) hydrogen bonds : angle 5.70086 ( 2158) metal coordination : bond 0.03287 ( 8) metal coordination : angle 4.27751 ( 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 276 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 219 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 494 ARG cc_start: 0.7891 (ptt-90) cc_final: 0.7686 (ptt-90) REVERT: A 531 ASP cc_start: 0.7727 (t0) cc_final: 0.7434 (t0) REVERT: A 731 ASP cc_start: 0.7831 (p0) cc_final: 0.7584 (p0) REVERT: A 743 PHE cc_start: 0.7884 (m-10) cc_final: 0.7581 (m-10) REVERT: A 828 ARG cc_start: 0.7837 (tpp80) cc_final: 0.7587 (ttm-80) REVERT: A 877 GLU cc_start: 0.7780 (tp30) cc_final: 0.7547 (tp30) REVERT: A 929 GLU cc_start: 0.6727 (tm-30) cc_final: 0.6366 (tm-30) REVERT: B 49 ASP cc_start: 0.7589 (m-30) cc_final: 0.7352 (m-30) REVERT: C 524 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8290 (tptt) REVERT: C 529 ARG cc_start: 0.7563 (mtp-110) cc_final: 0.7219 (ttp-170) REVERT: C 784 PHE cc_start: 0.8199 (t80) cc_final: 0.7749 (t80) REVERT: C 827 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7959 (tttm) REVERT: C 843 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8318 (pp) REVERT: D 5 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7376 (tpt) REVERT: D 143 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: D 237 ARG cc_start: 0.7738 (ttm110) cc_final: 0.7446 (ttm-80) REVERT: D 262 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8498 (mp) REVERT: D 280 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7094 (tp30) REVERT: D 298 GLU cc_start: 0.7273 (mp0) cc_final: 0.7017 (mp0) REVERT: D 349 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7189 (mmt90) outliers start: 57 outliers final: 27 residues processed: 253 average time/residue: 0.6101 time to fit residues: 173.8081 Evaluate side-chains 233 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 B residue 28 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 291 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 827 LYS Chi-restraints excluded: chain C residue 839 LYS Chi-restraints excluded: chain C residue 843 LEU 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 5 MET 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 242 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 B 173 ASN D 23 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3908 r_free = 0.3908 target = 0.156390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132550 restraints weight = 19987.388| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.52 r_work: 0.3516 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17152 Z= 0.186 Angle : 0.653 9.495 23657 Z= 0.346 Chirality : 0.043 0.172 2584 Planarity : 0.004 0.054 2643 Dihedral : 22.059 179.934 3170 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 2.93 % Allowed : 26.02 % Favored : 71.06 % 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: -1.25 (0.20), residues: 1766 helix: 0.32 (0.21), residues: 579 sheet: -2.33 (0.27), residues: 284 loop : -1.01 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 529 TYR 0.029 0.002 TYR A 514 PHE 0.016 0.002 PHE A 911 TRP 0.012 0.002 TRP B 307 HIS 0.005 0.001 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00420 (17144) covalent geometry : angle 0.65056 (23653) hydrogen bonds : bond 0.03980 ( 775) hydrogen bonds : angle 5.68788 ( 2158) metal coordination : bond 0.03121 ( 8) metal coordination : angle 4.00131 ( 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 262 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7715 (t0) cc_final: 0.7439 (t0) REVERT: A 731 ASP cc_start: 0.7791 (p0) cc_final: 0.7542 (p0) REVERT: A 743 PHE cc_start: 0.7822 (m-10) cc_final: 0.7513 (m-10) REVERT: A 877 GLU cc_start: 0.7821 (tp30) cc_final: 0.7601 (tp30) REVERT: A 929 GLU cc_start: 0.6680 (tm-30) cc_final: 0.6390 (tm-30) REVERT: B 49 ASP cc_start: 0.7637 (m-30) cc_final: 0.7379 (m-30) REVERT: B 162 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8090 (mpp) REVERT: C 524 LYS cc_start: 0.8399 (ttpt) cc_final: 0.8199 (tttp) REVERT: C 529 ARG cc_start: 0.7602 (mtp-110) cc_final: 0.7178 (ttp-170) REVERT: C 743 PHE cc_start: 0.8611 (m-80) cc_final: 0.8273 (m-80) REVERT: C 827 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8038 (tttm) REVERT: C 843 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8325 (pp) REVERT: D 143 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: D 237 ARG cc_start: 0.7715 (ttm110) cc_final: 0.7429 (ttm-80) REVERT: D 262 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8519 (mp) REVERT: D 280 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6985 (tp30) REVERT: D 285 MET cc_start: 0.8784 (mmm) cc_final: 0.8407 (mmm) REVERT: D 298 GLU cc_start: 0.7286 (mp0) cc_final: 0.7024 (mp0) outliers start: 46 outliers final: 28 residues processed: 246 average time/residue: 0.5654 time to fit residues: 156.4603 Evaluate side-chains 236 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 726 ILE 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 162 MET Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 827 LYS Chi-restraints excluded: chain C residue 839 LYS Chi-restraints excluded: chain C residue 843 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 146 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 47 optimal weight: 0.0270 chunk 13 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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** A 830 GLN ** 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 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 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 = 0.3925 r_free = 0.3925 target = 0.157787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.133962 restraints weight = 19997.741| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.52 r_work: 0.3536 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17152 Z= 0.174 Angle : 0.644 8.977 23657 Z= 0.342 Chirality : 0.043 0.166 2584 Planarity : 0.004 0.050 2643 Dihedral : 22.021 179.324 3170 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 2.86 % Allowed : 26.27 % Favored : 70.87 % 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: -1.20 (0.20), residues: 1766 helix: 0.34 (0.21), residues: 579 sheet: -2.30 (0.27), residues: 287 loop : -0.96 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 529 TYR 0.026 0.002 TYR A 514 PHE 0.013 0.001 PHE B 48 TRP 0.011 0.002 TRP D 307 HIS 0.006 0.001 HIS C 818 Details of bonding type rmsd covalent geometry : bond 0.00392 (17144) covalent geometry : angle 0.64288 (23653) hydrogen bonds : bond 0.03872 ( 775) hydrogen bonds : angle 5.64706 ( 2158) metal coordination : bond 0.02807 ( 8) metal coordination : angle 3.53699 ( 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 260 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7676 (t0) cc_final: 0.7391 (t0) REVERT: A 731 ASP cc_start: 0.7759 (p0) cc_final: 0.7506 (p0) REVERT: A 743 PHE cc_start: 0.7763 (m-10) cc_final: 0.7519 (m-10) REVERT: A 827 LYS cc_start: 0.8662 (tptm) cc_final: 0.8353 (tttp) REVERT: A 877 GLU cc_start: 0.7818 (tp30) cc_final: 0.7565 (tp30) REVERT: A 929 GLU cc_start: 0.6639 (tm-30) cc_final: 0.6312 (tm-30) REVERT: B 49 ASP cc_start: 0.7583 (m-30) cc_final: 0.7352 (m-30) REVERT: B 162 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8096 (mpp) REVERT: C 529 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.7142 (ttp-170) REVERT: C 572 GLU cc_start: 0.7548 (mp0) cc_final: 0.7252 (mm-30) REVERT: C 617 GLU cc_start: 0.7885 (mm-30) cc_final: 0.6983 (tt0) REVERT: C 743 PHE cc_start: 0.8560 (m-80) cc_final: 0.8306 (m-80) REVERT: C 784 PHE cc_start: 0.8200 (t80) cc_final: 0.7722 (t80) REVERT: C 827 LYS cc_start: 0.8433 (tttt) cc_final: 0.8015 (tttm) REVERT: C 843 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8286 (pp) REVERT: D 143 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7105 (m-30) REVERT: D 237 ARG cc_start: 0.7686 (ttm110) cc_final: 0.7397 (ttm-80) REVERT: D 262 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8494 (mp) REVERT: D 280 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6965 (tp30) REVERT: D 298 GLU cc_start: 0.7296 (mp0) cc_final: 0.7038 (mp0) REVERT: D 349 ARG cc_start: 0.7488 (mtp-110) cc_final: 0.7193 (mmt90) outliers start: 45 outliers final: 26 residues processed: 244 average time/residue: 0.5567 time to fit residues: 153.8029 Evaluate side-chains 236 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 726 ILE 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 162 MET 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 291 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 818 HIS Chi-restraints excluded: chain C residue 839 LYS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 262 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 174 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** A 830 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 HIS D 23 ASN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3899 r_free = 0.3899 target = 0.155447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.131429 restraints weight = 19742.368| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.51 r_work: 0.3489 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17152 Z= 0.224 Angle : 0.672 8.841 23657 Z= 0.355 Chirality : 0.044 0.170 2584 Planarity : 0.005 0.050 2643 Dihedral : 22.082 179.542 3170 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 2.80 % Allowed : 26.72 % Favored : 70.48 % 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: 0.32 (0.21), residues: 579 sheet: -2.32 (0.27), residues: 299 loop : -0.91 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 529 TYR 0.025 0.002 TYR A 514 PHE 0.020 0.002 PHE A 911 TRP 0.016 0.002 TRP C 829 HIS 0.010 0.002 HIS C 818 Details of bonding type rmsd covalent geometry : bond 0.00508 (17144) covalent geometry : angle 0.66960 (23653) hydrogen bonds : bond 0.04264 ( 775) hydrogen bonds : angle 5.71033 ( 2158) metal coordination : bond 0.03801 ( 8) metal coordination : angle 4.20786 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5606.46 seconds wall clock time: 96 minutes 47.94 seconds (5807.94 seconds total)