Starting phenix.real_space_refine on Sat Sep 12 14:49:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xny_22273/09_2026/6xny_22273.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xny_22273/09_2026/6xny_22273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xny_22273/09_2026/6xny_22273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xny_22273/09_2026/6xny_22273.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xny_22273/09_2026/6xny_22273.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xny_22273/09_2026/6xny_22273.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xny_22273/09_2026/6xny_22273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xny_22273/09_2026/6xny_22273.cif" } resolution = 2.9 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= 0.007 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 116 5.49 5 Mg 4 5.21 5 S 105 5.16 5 C 10185 2.51 5 N 2916 2.21 5 O 3353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16681 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4411 Classifications: {'peptide': 550} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 524} Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2689 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4398 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 522} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2694 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "x" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 704 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain: "y" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} 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: 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2082 SG CYS A 727 66.873 86.313 62.509 1.00 36.42 S ATOM 2103 SG CYS A 730 66.952 89.863 64.855 1.00 36.29 S ATOM 9178 SG CYS C 727 65.459 21.965 62.339 1.00 35.42 S ATOM 9199 SG CYS C 730 65.287 18.415 64.592 1.00 34.95 S Time building chain proxies: 2.82, per 1000 atoms: 0.17 Number of scatterers: 16681 At special positions: 0 Unit cell: (132.3, 108.15, 114.45, 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 105 16.00 P 116 15.00 Mg 4 11.99 O 3353 8.00 N 2916 7.00 C 10185 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: 1.16 Conformation dependent library (CDL) restraints added in 536.5 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 C1103 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 937 " Number of angles added : 4 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3344 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 22 sheets defined 35.9% alpha, 20.9% beta 58 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 2.32 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: 3.788A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 581 removed outlier: 5.238A pdb=" N GLU A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASP A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) 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 777 Processing helix chain 'A' and resid 792 through 814 Processing helix chain 'A' and resid 822 through 840 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 868 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 907 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: 3.793A 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 1004 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.631A 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: 3.945A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 580 Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 735 through 740 removed outlier: 3.618A pdb=" N ASN C 740 " --> pdb=" O GLU C 736 " (cutoff:3.500A) 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 812 Processing helix chain 'C' and resid 822 through 840 Processing helix chain 'C' and resid 852 through 857 Processing helix chain 'C' and resid 859 through 868 removed outlier: 3.601A pdb=" N GLU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 890 Processing helix chain 'C' and resid 891 through 893 No H-bonds generated for 'chain 'C' and resid 891 through 893' 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 924 through 929 removed outlier: 3.634A pdb=" N GLU C 929 " --> pdb=" O LYS C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.659A pdb=" N LYS C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 995 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 534 through 536 removed outlier: 6.234A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N CYS A 652 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 626 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 601 through 603 removed outlier: 5.128A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 628 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.601A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL B 8 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N PHE B 343 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 21 through 24 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.824A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.080A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 146 Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 208 through 212 Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.734A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 262 through 267 removed outlier: 7.335A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 277 through 279 Processing sheet with id=AB4, first strand: chain 'C' and resid 517 through 519 removed outlier: 3.621A pdb=" N THR C 630 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 517 through 519 removed outlier: 3.621A pdb=" N THR C 630 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.029A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 8 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE D 343 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.469A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.326A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 137 through 138 Processing sheet with id=AC1, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AC2, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.941A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 270 through 273 Processing sheet with id=AC4, first strand: chain 'D' and resid 277 through 279 641 hydrogen bonds defined for protein. 1776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 148 hydrogen bonds 296 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2457 1.29 - 1.42: 5098 1.42 - 1.55: 9355 1.55 - 1.68: 232 1.68 - 1.81: 162 Bond restraints: 17304 Sorted by residual: bond pdb=" C PRO A 891 " pdb=" O PRO A 891 " ideal model delta sigma weight residual 1.238 1.160 0.078 1.33e-02 5.65e+03 3.44e+01 bond pdb=" C3' DC y 45 " pdb=" O3' DC y 45 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.05e+01 bond pdb=" O3' DC y 45 " pdb=" P DC y 46 " ideal model delta sigma weight residual 1.607 1.560 0.047 1.20e-02 6.94e+03 1.54e+01 bond pdb=" O3' DT M 22 " pdb=" P DG M 23 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.20e-02 6.94e+03 1.43e+01 bond pdb=" C3' DG x 44 " pdb=" O3' DG x 44 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.27e+01 ... (remaining 17299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 23255 2.38 - 4.76: 617 4.76 - 7.14: 23 7.14 - 9.51: 8 9.51 - 11.89: 3 Bond angle restraints: 23906 Sorted by residual: angle pdb=" N ASN D 335 " pdb=" CA ASN D 335 " pdb=" C ASN D 335 " ideal model delta sigma weight residual 111.04 99.15 11.89 1.55e+00 4.16e-01 5.89e+01 angle pdb=" C GLN C 520 " pdb=" CA GLN C 520 " pdb=" CB GLN C 520 " ideal model delta sigma weight residual 110.17 121.40 -11.23 1.97e+00 2.58e-01 3.25e+01 angle pdb=" O4' DC y 36 " pdb=" C4' DC y 36 " pdb=" C3' DC y 36 " ideal model delta sigma weight residual 106.00 102.90 3.10 6.00e-01 2.78e+00 2.67e+01 angle pdb=" O4' DT x 45 " pdb=" C4' DT x 45 " pdb=" C3' DT x 45 " ideal model delta sigma weight residual 106.00 102.98 3.02 6.00e-01 2.78e+00 2.53e+01 angle pdb=" N3 DT x 53 " pdb=" C4 DT x 53 " pdb=" O4 DT x 53 " ideal model delta sigma weight residual 119.90 122.89 -2.99 6.00e-01 2.78e+00 2.48e+01 ... (remaining 23901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.11: 9335 34.11 - 68.22: 708 68.22 - 102.33: 22 102.33 - 136.44: 0 136.44 - 170.55: 5 Dihedral angle restraints: 10070 sinusoidal: 4877 harmonic: 5193 Sorted by residual: dihedral pdb=" C ASN B 101 " pdb=" N ASN B 101 " pdb=" CA ASN B 101 " pdb=" CB ASN B 101 " ideal model delta harmonic sigma weight residual -122.60 -136.24 13.64 0 2.50e+00 1.60e-01 2.98e+01 dihedral pdb=" C GLN C 520 " pdb=" N GLN C 520 " pdb=" CA GLN C 520 " pdb=" CB GLN C 520 " ideal model delta harmonic sigma weight residual -122.60 -136.13 13.53 0 2.50e+00 1.60e-01 2.93e+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 -152.94 -27.06 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 10067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2323 0.092 - 0.185: 239 0.185 - 0.277: 41 0.277 - 0.370: 7 0.370 - 0.462: 2 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CA ASN B 101 " pdb=" N ASN B 101 " pdb=" C ASN B 101 " pdb=" CB ASN B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA GLN C 520 " pdb=" N GLN C 520 " pdb=" C GLN C 520 " pdb=" CB GLN C 520 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+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 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 2609 not shown) Planarity restraints: 2655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 773 " 0.313 9.50e-02 1.11e+02 1.40e-01 1.21e+01 pdb=" NE ARG A 773 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 773 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 773 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 773 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA y 30 " 0.043 2.00e-02 2.50e+03 1.93e-02 1.02e+01 pdb=" N9 DA y 30 " -0.041 2.00e-02 2.50e+03 pdb=" C8 DA y 30 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA y 30 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA y 30 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA y 30 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA y 30 " 0.020 2.00e-02 2.50e+03 pdb=" N1 DA y 30 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA y 30 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA y 30 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA y 30 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT x 43 " 0.038 2.00e-02 2.50e+03 1.76e-02 7.78e+00 pdb=" N1 DT x 43 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DT x 43 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT x 43 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT x 43 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT x 43 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT x 43 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT x 43 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT x 43 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT x 43 " -0.009 2.00e-02 2.50e+03 ... (remaining 2652 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 31 2.28 - 2.93: 8234 2.93 - 3.59: 28144 3.59 - 4.24: 49319 4.24 - 4.90: 76973 Nonbonded interactions: 162701 Sorted by model distance: nonbonded pdb=" O GLY A 601 " pdb="MG MG A1101 " model vdw 1.619 2.170 nonbonded pdb=" OE2 GLU C 662 " pdb="MG MG C1102 " model vdw 1.816 2.170 nonbonded pdb=" OD2 ASP C 708 " pdb="MG MG C1102 " model vdw 1.898 2.170 nonbonded pdb=" OP2 DC x 47 " pdb="MG MG C1101 " model vdw 2.018 2.170 nonbonded pdb=" OD1 ASP C 600 " pdb="MG MG C1101 " model vdw 2.080 2.170 ... (remaining 162696 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 1006 or (resid 1007 and (name N or name CA or \ name C or name O or name CB )) or resid 1101 through 1103)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 1 through 116 or (resid 117 through 118 and (name N or nam \ e CA or name C or name O or name CB )) or resid 119 through 350)) selection = (chain 'D' and (resid 1 through 336 or (resid 337 through 339 and (name N or nam \ e CA or name C or name O or name CB )) or resid 340 through 350)) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'x' and ((resid 35 and (name O5' or name C5' or name C4' or name O4' or n \ ame C3' or name O3' or name C2' or name C1' or name N9 or name C8 or name N7 or \ name C5 or name C6 or name N6 or name N1 or name C2 or name N3 or name C4 )) or \ resid 36 through 48 or resid 50 through 65)) selection = (chain 'y' and (resid 24 through 37 or resid 39 through 54)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 18.290 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.012 0.658 17312 Z= 0.594 Angle : 0.993 45.170 23910 Z= 0.601 Chirality : 0.063 0.462 2612 Planarity : 0.005 0.140 2655 Dihedral : 20.646 170.550 6726 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.01 % Favored : 90.93 % Rotamer: Outliers : 3.25 % Allowed : 13.70 % Favored : 83.05 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.16), residues: 1775 helix: -2.62 (0.16), residues: 573 sheet: -3.59 (0.23), residues: 322 loop : -2.99 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 159 TYR 0.030 0.002 TYR D 195 PHE 0.015 0.002 PHE B 206 TRP 0.011 0.002 TRP C 893 HIS 0.012 0.001 HIS C 937 Details of bonding type rmsd/Z covalent geometry : bond 0.01063 / 0.58 (17304) covalent geometry : angle 0.86824 / 0.59 (23906) hydrogen bonds : bond 0.13843 / 9.33 ( 761) hydrogen bonds : angle 8.04285 / 5.51 ( 2072) metal coordination : bond 0.25980 / 15.51 ( 8) metal coordination : angle 37.22816 / 17.52 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8848 (m) REVERT: B 1 MET cc_start: 0.4432 (OUTLIER) cc_final: 0.3921 (ptm) REVERT: B 186 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6690 (p0) REVERT: C 573 ASP cc_start: 0.7547 (m-30) cc_final: 0.7347 (m-30) REVERT: C 724 VAL cc_start: 0.8544 (p) cc_final: 0.8266 (m) REVERT: C 847 MET cc_start: 0.7376 (ttp) cc_final: 0.6971 (ttp) REVERT: D 20 SER cc_start: 0.8237 (m) cc_final: 0.7759 (p) REVERT: D 80 TYR cc_start: 0.6675 (m-80) cc_final: 0.6471 (m-80) REVERT: D 164 SER cc_start: 0.7769 (OUTLIER) cc_final: 0.7406 (p) REVERT: D 234 TYR cc_start: 0.7775 (m-80) cc_final: 0.7561 (m-80) outliers start: 51 outliers final: 25 residues processed: 349 average time/residue: 0.5311 time to fit residues: 207.6550 Evaluate side-chains 235 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 958 SER Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 HIS A 633 HIS A 740 ASN B 33 GLN B 53 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN C 609 HIS C 820 ASN D 53 ASN D 337 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132438 restraints weight = 20744.570| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.44 r_work: 0.3490 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 17312 Z= 0.236 Angle : 0.774 18.225 23910 Z= 0.414 Chirality : 0.049 0.383 2612 Planarity : 0.005 0.044 2655 Dihedral : 22.643 175.568 3279 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 4.65 % Allowed : 19.57 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.18), residues: 1775 helix: -1.31 (0.18), residues: 589 sheet: -3.38 (0.24), residues: 325 loop : -2.10 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 529 TYR 0.022 0.002 TYR C 725 PHE 0.022 0.002 PHE B 206 TRP 0.013 0.002 TRP A 992 HIS 0.009 0.001 HIS C 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (17304) covalent geometry : angle 0.75588 / 0.41 (23906) hydrogen bonds : bond 0.05713 / 3.89 ( 761) hydrogen bonds : angle 6.58055 / 4.49 ( 2072) metal coordination : bond 0.07903 / 4.89 ( 8) metal coordination : angle 13.04128 / 6.90 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 243 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7820 (mm-40) REVERT: A 658 MET cc_start: 0.8612 (mtm) cc_final: 0.8391 (mtm) REVERT: A 731 ASP cc_start: 0.8285 (p0) cc_final: 0.8046 (p0) REVERT: A 847 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7314 (ttm) REVERT: B 1 MET cc_start: 0.5082 (ptt) cc_final: 0.4565 (ptm) REVERT: B 4 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7253 (tm-30) REVERT: B 53 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.7288 (m-40) REVERT: B 282 GLN cc_start: 0.7278 (tp40) cc_final: 0.6915 (tm130) REVERT: C 573 ASP cc_start: 0.8327 (m-30) cc_final: 0.7950 (m-30) REVERT: C 627 MET cc_start: 0.8818 (mmm) cc_final: 0.8598 (mmm) REVERT: C 716 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7630 (tp30) REVERT: C 736 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: C 828 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7223 (mtp85) REVERT: C 877 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: C 883 MET cc_start: 0.8608 (tpp) cc_final: 0.8211 (tpp) outliers start: 73 outliers final: 24 residues processed: 289 average time/residue: 0.4767 time to fit residues: 157.2902 Evaluate side-chains 227 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 728 THR Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 877 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 216 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 130 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN A 990 HIS B 33 GLN C 473 ASN C 647 ASN C 914 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.155745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134759 restraints weight = 21016.656| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.41 r_work: 0.3521 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 17312 Z= 0.189 Angle : 0.714 12.618 23910 Z= 0.385 Chirality : 0.047 0.360 2612 Planarity : 0.005 0.040 2655 Dihedral : 22.575 174.591 3249 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.82 % Allowed : 21.86 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.19), residues: 1775 helix: -0.74 (0.19), residues: 591 sheet: -3.20 (0.23), residues: 345 loop : -1.71 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 696 TYR 0.024 0.002 TYR C 886 PHE 0.019 0.002 PHE C 591 TRP 0.011 0.002 TRP D 307 HIS 0.007 0.001 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (17304) covalent geometry : angle 0.70515 / 0.38 (23906) hydrogen bonds : bond 0.04903 / 3.33 ( 761) hydrogen bonds : angle 6.27072 / 4.28 ( 2072) metal coordination : bond 0.05556 / 3.50 ( 8) metal coordination : angle 8.57811 / 4.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7874 (mm-40) REVERT: A 691 MET cc_start: 0.8786 (ptp) cc_final: 0.8581 (ptm) REVERT: B 1 MET cc_start: 0.5094 (ptt) cc_final: 0.4565 (ptm) REVERT: B 5 MET cc_start: 0.7697 (ttm) cc_final: 0.7281 (ttt) REVERT: B 282 GLN cc_start: 0.7243 (tp40) cc_final: 0.6915 (tm130) REVERT: C 573 ASP cc_start: 0.8290 (m-30) cc_final: 0.7914 (m-30) REVERT: C 716 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7587 (tp30) REVERT: C 824 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7464 (mm-30) REVERT: C 828 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7137 (mtp85) REVERT: C 843 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8262 (pp) REVERT: C 874 GLU cc_start: 0.7708 (pp20) cc_final: 0.7438 (tm-30) REVERT: C 901 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.7010 (mt-10) outliers start: 60 outliers final: 19 residues processed: 282 average time/residue: 0.4829 time to fit residues: 155.1181 Evaluate side-chains 232 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 901 GLU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 322 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 165 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 183 optimal weight: 50.0000 chunk 67 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN B 232 ASN C 800 ASN C 914 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.155999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135273 restraints weight = 20925.682| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.38 r_work: 0.3525 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 17312 Z= 0.189 Angle : 0.694 11.631 23910 Z= 0.375 Chirality : 0.048 0.378 2612 Planarity : 0.005 0.039 2655 Dihedral : 22.557 173.501 3245 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer: Outliers : 4.21 % Allowed : 23.39 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.19), residues: 1775 helix: -0.47 (0.20), residues: 594 sheet: -3.01 (0.24), residues: 334 loop : -1.52 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 696 TYR 0.023 0.002 TYR D 234 PHE 0.016 0.002 PHE C 591 TRP 0.022 0.002 TRP A 956 HIS 0.007 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (17304) covalent geometry : angle 0.68757 / 0.37 (23906) hydrogen bonds : bond 0.04707 / 3.20 ( 761) hydrogen bonds : angle 6.08954 / 4.14 ( 2072) metal coordination : bond 0.05155 / 3.21 ( 8) metal coordination : angle 7.32803 / 3.35 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 232 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7905 (mm-40) REVERT: A 667 THR cc_start: 0.8979 (m) cc_final: 0.8573 (p) REVERT: A 774 ASP cc_start: 0.7587 (t70) cc_final: 0.7346 (t0) REVERT: A 931 LYS cc_start: 0.7907 (ptmm) cc_final: 0.7591 (pttt) REVERT: B 1 MET cc_start: 0.5090 (ptt) cc_final: 0.4573 (ptm) REVERT: B 143 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: B 282 GLN cc_start: 0.7198 (tp40) cc_final: 0.6902 (tm130) REVERT: C 573 ASP cc_start: 0.8245 (m-30) cc_final: 0.7896 (m-30) REVERT: C 584 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6379 (p0) REVERT: C 736 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: C 828 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7314 (mtp85) REVERT: C 843 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8167 (pp) REVERT: D 141 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8308 (t) outliers start: 66 outliers final: 27 residues processed: 282 average time/residue: 0.5552 time to fit residues: 178.3239 Evaluate side-chains 239 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 322 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 82 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 183 optimal weight: 50.0000 chunk 175 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN C 525 ASN C 753 ASN C 800 ASN C 914 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.155434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134331 restraints weight = 20898.216| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.38 r_work: 0.3513 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 17312 Z= 0.199 Angle : 0.695 11.925 23910 Z= 0.374 Chirality : 0.047 0.366 2612 Planarity : 0.005 0.035 2655 Dihedral : 22.576 173.438 3244 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.97 % Rotamer: Outliers : 4.40 % Allowed : 23.77 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.19), residues: 1775 helix: -0.29 (0.20), residues: 594 sheet: -2.97 (0.23), residues: 339 loop : -1.42 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 529 TYR 0.021 0.002 TYR D 234 PHE 0.018 0.002 PHE D 271 TRP 0.012 0.002 TRP A 956 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (17304) covalent geometry : angle 0.68947 / 0.37 (23906) hydrogen bonds : bond 0.04642 / 3.14 ( 761) hydrogen bonds : angle 5.98930 / 4.06 ( 2072) metal coordination : bond 0.04807 / 2.95 ( 8) metal coordination : angle 7.09477 / 3.27 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 234 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8159 (ptp) REVERT: A 774 ASP cc_start: 0.7719 (t70) cc_final: 0.7422 (t0) REVERT: A 931 LYS cc_start: 0.8049 (ptmm) cc_final: 0.7729 (pttt) REVERT: B 1 MET cc_start: 0.5087 (ptt) cc_final: 0.4573 (ptm) REVERT: B 143 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: B 282 GLN cc_start: 0.7218 (tp40) cc_final: 0.6921 (tm130) REVERT: C 508 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7897 (mppt) REVERT: C 573 ASP cc_start: 0.8267 (m-30) cc_final: 0.7910 (m-30) REVERT: C 584 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6465 (p0) REVERT: C 699 LYS cc_start: 0.8295 (mttp) cc_final: 0.8007 (mmtt) REVERT: C 736 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: C 828 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7328 (mtp85) REVERT: C 843 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8207 (pp) REVERT: C 847 MET cc_start: 0.8004 (ttm) cc_final: 0.7772 (ttm) REVERT: D 80 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.5916 (m-80) REVERT: D 141 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8350 (t) REVERT: D 166 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: D 237 ARG cc_start: 0.7259 (ttm110) cc_final: 0.7028 (ttm110) outliers start: 69 outliers final: 33 residues processed: 279 average time/residue: 0.5085 time to fit residues: 161.3606 Evaluate side-chains 250 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 322 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 chunk 123 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 183 optimal weight: 50.0000 chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1004 ASN B 33 GLN C 753 ASN C 800 ASN C 914 GLN D 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136969 restraints weight = 20826.661| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.41 r_work: 0.3547 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17312 Z= 0.166 Angle : 0.679 11.920 23910 Z= 0.367 Chirality : 0.046 0.362 2612 Planarity : 0.004 0.038 2655 Dihedral : 22.489 173.921 3242 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.89 % Allowed : 24.67 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.19), residues: 1775 helix: -0.11 (0.20), residues: 597 sheet: -2.83 (0.24), residues: 329 loop : -1.35 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 529 TYR 0.019 0.002 TYR D 234 PHE 0.017 0.002 PHE D 271 TRP 0.013 0.001 TRP A 956 HIS 0.005 0.001 HIS D 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (17304) covalent geometry : angle 0.67476 / 0.37 (23906) hydrogen bonds : bond 0.04339 / 2.95 ( 761) hydrogen bonds : angle 5.83648 / 3.94 ( 2072) metal coordination : bond 0.03704 / 2.25 ( 8) metal coordination : angle 6.08175 / 2.87 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 244 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8195 (ptp) REVERT: A 774 ASP cc_start: 0.7710 (t70) cc_final: 0.7403 (t0) REVERT: A 931 LYS cc_start: 0.8028 (ptmm) cc_final: 0.7757 (pttt) REVERT: B 1 MET cc_start: 0.5125 (ptt) cc_final: 0.4603 (ptm) REVERT: B 5 MET cc_start: 0.7624 (ttm) cc_final: 0.7376 (mtt) REVERT: B 58 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8138 (pttt) REVERT: B 143 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: B 282 GLN cc_start: 0.7211 (tp40) cc_final: 0.6910 (tm130) REVERT: C 508 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7755 (mppt) REVERT: C 573 ASP cc_start: 0.8269 (m-30) cc_final: 0.7894 (m-30) REVERT: C 584 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6456 (p0) REVERT: C 736 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: C 828 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7327 (mtp85) REVERT: C 843 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8142 (pp) REVERT: C 963 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8370 (m) REVERT: D 80 TYR cc_start: 0.6596 (OUTLIER) cc_final: 0.5793 (m-10) REVERT: D 237 ARG cc_start: 0.7175 (ttm110) cc_final: 0.6839 (ttm110) outliers start: 61 outliers final: 28 residues processed: 282 average time/residue: 0.4762 time to fit residues: 153.9480 Evaluate side-chains 253 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 322 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 155 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS C 914 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.127204 restraints weight = 21093.091| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.42 r_work: 0.3407 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 17312 Z= 0.340 Angle : 0.784 11.190 23910 Z= 0.415 Chirality : 0.051 0.378 2612 Planarity : 0.005 0.043 2655 Dihedral : 22.804 173.692 3242 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.42 % Favored : 93.52 % Rotamer: Outliers : 4.46 % Allowed : 24.22 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.19), residues: 1775 helix: -0.31 (0.20), residues: 590 sheet: -2.75 (0.24), residues: 328 loop : -1.45 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 855 TYR 0.023 0.002 TYR A 725 PHE 0.019 0.003 PHE A 698 TRP 0.013 0.002 TRP C 992 HIS 0.009 0.002 HIS D 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.34 (17304) covalent geometry : angle 0.77767 / 0.41 (23906) hydrogen bonds : bond 0.05656 / 3.75 ( 761) hydrogen bonds : angle 6.07434 / 4.11 ( 2072) metal coordination : bond 0.06022 / 3.59 ( 8) metal coordination : angle 7.45334 / 3.45 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8226 (ptp) REVERT: A 662 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7005 (pp20) REVERT: A 774 ASP cc_start: 0.7944 (t70) cc_final: 0.7637 (t0) REVERT: A 931 LYS cc_start: 0.8158 (ptmm) cc_final: 0.7862 (pttt) REVERT: B 1 MET cc_start: 0.5044 (ptt) cc_final: 0.4472 (ptm) REVERT: B 5 MET cc_start: 0.8028 (ttm) cc_final: 0.7817 (mtt) REVERT: B 143 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: B 322 MET cc_start: 0.8533 (mtp) cc_final: 0.8260 (mtm) REVERT: C 494 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7398 (mtm-85) REVERT: C 508 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8346 (mppt) REVERT: C 573 ASP cc_start: 0.8413 (m-30) cc_final: 0.7892 (m-30) REVERT: C 584 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6584 (p0) REVERT: C 736 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: C 828 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7457 (mtp85) REVERT: C 843 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8389 (pp) REVERT: D 4 GLN cc_start: 0.6843 (pm20) cc_final: 0.6606 (pm20) REVERT: D 80 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: D 166 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: D 179 LEU cc_start: 0.8320 (mt) cc_final: 0.8117 (mt) REVERT: D 195 TYR cc_start: 0.8354 (m-80) cc_final: 0.8104 (m-80) outliers start: 70 outliers final: 42 residues processed: 262 average time/residue: 0.5289 time to fit residues: 157.7221 Evaluate side-chains 250 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 787 THR Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 326 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 128 optimal weight: 0.7980 chunk 152 optimal weight: 0.0030 chunk 29 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 64 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 overall best weight: 0.5128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 665 HIS B 4 GLN B 33 GLN B 282 GLN C 914 GLN ** D 207 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 = 0.3891 r_free = 0.3891 target = 0.156536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135301 restraints weight = 21277.268| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.44 r_work: 0.3530 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17312 Z= 0.166 Angle : 0.690 9.210 23910 Z= 0.372 Chirality : 0.047 0.361 2612 Planarity : 0.004 0.040 2655 Dihedral : 22.531 175.414 3242 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 3.57 % Allowed : 26.13 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.19), residues: 1775 helix: -0.11 (0.20), residues: 594 sheet: -2.87 (0.24), residues: 311 loop : -1.34 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 679 TYR 0.018 0.002 TYR D 344 PHE 0.022 0.002 PHE D 271 TRP 0.016 0.002 TRP A 956 HIS 0.007 0.001 HIS D 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (17304) covalent geometry : angle 0.68667 / 0.37 (23906) hydrogen bonds : bond 0.04327 / 2.91 ( 761) hydrogen bonds : angle 5.87820 / 3.97 ( 2072) metal coordination : bond 0.03128 / 1.85 ( 8) metal coordination : angle 5.58603 / 2.78 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7258 (p0) cc_final: 0.6933 (p0) REVERT: A 774 ASP cc_start: 0.7849 (t70) cc_final: 0.7570 (t0) REVERT: A 931 LYS cc_start: 0.8064 (ptmm) cc_final: 0.7799 (pttt) REVERT: B 1 MET cc_start: 0.5088 (ptt) cc_final: 0.4549 (ptm) REVERT: B 4 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7042 (tp40) REVERT: B 5 MET cc_start: 0.7649 (ttm) cc_final: 0.7166 (mtt) REVERT: B 143 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: B 334 ASP cc_start: 0.5701 (p0) cc_final: 0.5393 (t0) REVERT: C 494 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7299 (mtm-85) REVERT: C 573 ASP cc_start: 0.8320 (m-30) cc_final: 0.7780 (m-30) REVERT: C 584 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6651 (p0) REVERT: C 699 LYS cc_start: 0.8358 (mttp) cc_final: 0.8080 (mmtt) REVERT: C 736 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: C 828 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7402 (mtp85) REVERT: C 843 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8229 (pp) REVERT: C 963 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8448 (m) REVERT: D 4 GLN cc_start: 0.6828 (pm20) cc_final: 0.6570 (pm20) REVERT: D 80 TYR cc_start: 0.6246 (OUTLIER) cc_final: 0.5689 (m-10) REVERT: D 195 TYR cc_start: 0.8174 (m-80) cc_final: 0.7966 (m-80) REVERT: D 237 ARG cc_start: 0.7272 (ttm110) cc_final: 0.6901 (ttm110) REVERT: D 344 TYR cc_start: 0.7677 (m-10) cc_final: 0.7462 (m-10) outliers start: 56 outliers final: 32 residues processed: 272 average time/residue: 0.5234 time to fit residues: 162.6874 Evaluate side-chains 245 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 585 ASP Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 326 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 131 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 153 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.134997 restraints weight = 21246.030| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.44 r_work: 0.3520 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17312 Z= 0.177 Angle : 0.691 9.227 23910 Z= 0.372 Chirality : 0.047 0.364 2612 Planarity : 0.004 0.044 2655 Dihedral : 22.507 174.886 3242 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 3.25 % Allowed : 26.45 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.19), residues: 1775 helix: 0.02 (0.21), residues: 587 sheet: -2.79 (0.24), residues: 311 loop : -1.29 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 349 TYR 0.020 0.002 TYR D 234 PHE 0.038 0.002 PHE D 271 TRP 0.015 0.002 TRP C 893 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 (17304) covalent geometry : angle 0.68769 / 0.37 (23906) hydrogen bonds : bond 0.04343 / 2.93 ( 761) hydrogen bonds : angle 5.81716 / 3.91 ( 2072) metal coordination : bond 0.03339 / 1.95 ( 8) metal coordination : angle 5.16124 / 2.53 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 ASP cc_start: 0.7300 (p0) cc_final: 0.6982 (p0) REVERT: A 662 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.6962 (pp20) REVERT: A 690 GLU cc_start: 0.7837 (pp20) cc_final: 0.7047 (pm20) REVERT: A 774 ASP cc_start: 0.7798 (t70) cc_final: 0.7558 (t0) REVERT: A 931 LYS cc_start: 0.8091 (ptmm) cc_final: 0.7871 (pttt) REVERT: B 1 MET cc_start: 0.5092 (ptt) cc_final: 0.4533 (ptm) REVERT: B 4 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7204 (tp40) REVERT: B 5 MET cc_start: 0.7521 (ttm) cc_final: 0.7228 (mtt) REVERT: B 143 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: B 282 GLN cc_start: 0.7327 (tp40) cc_final: 0.7073 (tm-30) REVERT: B 334 ASP cc_start: 0.5706 (p0) cc_final: 0.5421 (t0) REVERT: C 573 ASP cc_start: 0.8280 (m-30) cc_final: 0.7748 (m-30) REVERT: C 828 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7432 (mtp85) REVERT: C 843 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8243 (pp) REVERT: C 847 MET cc_start: 0.7867 (ptp) cc_final: 0.7359 (ppp) REVERT: C 848 MET cc_start: 0.7566 (mpp) cc_final: 0.7245 (mpp) REVERT: C 963 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8416 (m) REVERT: D 4 GLN cc_start: 0.6818 (pm20) cc_final: 0.6566 (pm20) REVERT: D 80 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.5811 (m-10) REVERT: D 233 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7166 (tm) REVERT: D 344 TYR cc_start: 0.7723 (m-10) cc_final: 0.7522 (m-10) outliers start: 51 outliers final: 26 residues processed: 253 average time/residue: 0.5092 time to fit residues: 147.4143 Evaluate side-chains 244 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain C residue 585 ASP Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 38 optimal weight: 0.0000 chunk 106 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 169 optimal weight: 7.9990 chunk 21 optimal weight: 0.0980 chunk 7 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.158293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136939 restraints weight = 21266.439| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.45 r_work: 0.3549 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17312 Z= 0.162 Angle : 0.684 9.556 23910 Z= 0.370 Chirality : 0.047 0.363 2612 Planarity : 0.004 0.040 2655 Dihedral : 22.430 174.873 3240 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 2.23 % Allowed : 27.34 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.19), residues: 1775 helix: 0.07 (0.21), residues: 587 sheet: -2.72 (0.24), residues: 322 loop : -1.30 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 927 TYR 0.032 0.002 TYR C 928 PHE 0.029 0.002 PHE D 271 TRP 0.013 0.002 TRP A 956 HIS 0.007 0.001 HIS C 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (17304) covalent geometry : angle 0.68148 / 0.37 (23906) hydrogen bonds : bond 0.04249 / 2.89 ( 761) hydrogen bonds : angle 5.76618 / 3.88 ( 2072) metal coordination : bond 0.02882 / 1.67 ( 8) metal coordination : angle 4.89101 / 2.44 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 ARG cc_start: 0.7692 (mtm110) cc_final: 0.7415 (mtp85) REVERT: A 531 ASP cc_start: 0.7199 (p0) cc_final: 0.6904 (p0) REVERT: A 690 GLU cc_start: 0.7785 (pp20) cc_final: 0.6913 (pm20) REVERT: A 774 ASP cc_start: 0.7744 (t70) cc_final: 0.7483 (t0) REVERT: B 1 MET cc_start: 0.5053 (ptt) cc_final: 0.4507 (ptm) REVERT: B 4 GLN cc_start: 0.7593 (pt0) cc_final: 0.7254 (tp40) REVERT: B 5 MET cc_start: 0.7339 (ttm) cc_final: 0.7101 (mtt) REVERT: B 143 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: B 334 ASP cc_start: 0.5661 (p0) cc_final: 0.5320 (t0) REVERT: C 573 ASP cc_start: 0.8247 (m-30) cc_final: 0.7700 (m-30) REVERT: C 699 LYS cc_start: 0.8341 (mttp) cc_final: 0.8072 (mmtt) REVERT: C 828 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7520 (mtp85) REVERT: C 834 ASP cc_start: 0.8123 (m-30) cc_final: 0.7697 (m-30) REVERT: C 843 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8189 (pp) REVERT: C 847 MET cc_start: 0.7829 (ptp) cc_final: 0.7319 (ppp) REVERT: C 848 MET cc_start: 0.7412 (mpp) cc_final: 0.7211 (mpp) REVERT: C 963 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8362 (m) REVERT: D 80 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5673 (m-10) REVERT: D 233 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6971 (tm) outliers start: 35 outliers final: 24 residues processed: 250 average time/residue: 0.4910 time to fit residues: 141.8038 Evaluate side-chains 236 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain C residue 585 ASP Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 828 ARG Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 19 optimal weight: 0.0010 chunk 153 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 168 optimal weight: 0.2980 chunk 138 optimal weight: 0.6980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.160032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138938 restraints weight = 21262.643| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.44 r_work: 0.3578 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17312 Z= 0.157 Angle : 0.679 9.581 23910 Z= 0.367 Chirality : 0.046 0.362 2612 Planarity : 0.005 0.072 2655 Dihedral : 22.391 174.675 3240 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 2.68 % Allowed : 27.15 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.19), residues: 1775 helix: 0.14 (0.21), residues: 587 sheet: -2.66 (0.24), residues: 332 loop : -1.26 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 855 TYR 0.035 0.002 TYR C 928 PHE 0.024 0.002 PHE D 271 TRP 0.012 0.001 TRP A 956 HIS 0.006 0.001 HIS C 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (17304) covalent geometry : angle 0.67666 / 0.37 (23906) hydrogen bonds : bond 0.04198 / 2.85 ( 761) hydrogen bonds : angle 5.67984 / 3.80 ( 2072) metal coordination : bond 0.02599 / 1.50 ( 8) metal coordination : angle 4.34112 / 2.16 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5328.06 seconds wall clock time: 92 minutes 3.91 seconds (5523.91 seconds total)