Starting phenix.real_space_refine on Thu Mar 5 13:20:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d0z_27113/03_2026/8d0z_27113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d0z_27113/03_2026/8d0z_27113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d0z_27113/03_2026/8d0z_27113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d0z_27113/03_2026/8d0z_27113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d0z_27113/03_2026/8d0z_27113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d0z_27113/03_2026/8d0z_27113.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 14351 2.51 5 N 3751 2.21 5 O 4358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22566 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 6425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6425 Classifications: {'peptide': 824} Link IDs: {'PTRANS': 43, 'TRANS': 780} Chain breaks: 8 Chain: "A" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7939 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 54, 'TRANS': 960} Chain breaks: 7 Chain: "B" Number of atoms: 6395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6395 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 45, 'TRANS': 774} Chain breaks: 8 Chain: "H" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 763 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.78, per 1000 atoms: 0.21 Number of scatterers: 22566 At special positions: 0 Unit cell: (143.165, 140.03, 214.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 4358 8.00 N 3751 7.00 C 14351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 705 " - pdb=" SG CYS A 883 " distance=2.09 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS B 705 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.77 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=1.71 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.69 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 717 " " NAG B1301 " - " ASN B 717 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 331 " " NAG C1301 " - " ASN C 717 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1134 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 45 sheets defined 25.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 802 through 806 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 851 through 856 Processing helix chain 'C' and resid 866 through 882 Processing helix chain 'C' and resid 884 through 890 removed outlier: 3.548A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.502A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.048A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.646A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.106A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.810A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 888 No H-bonds generated for 'chain 'B' and resid 886 through 888' Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.506A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.728A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 96 through 100A Processing helix chain 'L' and resid 49 through 53 removed outlier: 4.222A pdb=" N ASN L 53 " --> pdb=" O ARG L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.761A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.116A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.515A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.895A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.387A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.284A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.620A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.390A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.441A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.441A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.829A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.416A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.441A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.725A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.804A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.422A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.247A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AC4, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.489A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.612A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.636A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.763A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.058A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.653A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.146A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.407A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.833A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.607A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.496A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.626A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.494A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.494A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.337A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.721A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.111A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.545A pdb=" N CYS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.635A pdb=" N HIS L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AE9, first strand: chain 'L' and resid 19 through 24 1075 hydrogen bonds defined for protein. 2913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4648 1.32 - 1.46: 8308 1.46 - 1.61: 9945 1.61 - 1.75: 31 1.75 - 1.90: 124 Bond restraints: 23056 Sorted by residual: bond pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 1.502 1.300 0.202 2.30e-02 1.89e+03 7.73e+01 bond pdb=" CB HIS A1064 " pdb=" CG HIS A1064 " ideal model delta sigma weight residual 1.497 1.382 0.115 1.40e-02 5.10e+03 6.79e+01 bond pdb=" CB PHE C 55 " pdb=" CG PHE C 55 " ideal model delta sigma weight residual 1.502 1.335 0.167 2.30e-02 1.89e+03 5.27e+01 bond pdb=" CB PHE B 888 " pdb=" CG PHE B 888 " ideal model delta sigma weight residual 1.502 1.353 0.149 2.30e-02 1.89e+03 4.18e+01 bond pdb=" CB ILE C 850 " pdb=" CG1 ILE C 850 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 23051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 28184 2.86 - 5.73: 2851 5.73 - 8.59: 285 8.59 - 11.45: 39 11.45 - 14.32: 3 Bond angle restraints: 31362 Sorted by residual: angle pdb=" N ASP L 26 " pdb=" CA ASP L 26 " pdb=" C ASP L 26 " ideal model delta sigma weight residual 112.38 98.06 14.32 1.22e+00 6.72e-01 1.38e+02 angle pdb=" C THR A 599 " pdb=" N PRO A 600 " pdb=" CA PRO A 600 " ideal model delta sigma weight residual 119.56 128.76 -9.20 1.02e+00 9.61e-01 8.14e+01 angle pdb=" N GLN A 613 " pdb=" CA GLN A 613 " pdb=" C GLN A 613 " ideal model delta sigma weight residual 111.28 120.73 -9.45 1.09e+00 8.42e-01 7.52e+01 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 111.41 98.47 12.94 1.50e+00 4.44e-01 7.44e+01 angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 119.78 128.61 -8.83 1.03e+00 9.43e-01 7.35e+01 ... (remaining 31357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13435 17.71 - 35.43: 359 35.43 - 53.14: 101 53.14 - 70.85: 30 70.85 - 88.57: 14 Dihedral angle restraints: 13939 sinusoidal: 5592 harmonic: 8347 Sorted by residual: dihedral pdb=" CB CYS A 705 " pdb=" SG CYS A 705 " pdb=" SG CYS B 883 " pdb=" CB CYS B 883 " ideal model delta sinusoidal sigma weight residual 93.00 146.44 -53.44 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" C ASN L 27 " pdb=" N ASN L 27 " pdb=" CA ASN L 27 " pdb=" CB ASN L 27 " ideal model delta harmonic sigma weight residual -122.60 -110.97 -11.63 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -119.41 33.41 1 1.00e+01 1.00e-02 1.59e+01 ... (remaining 13936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2684 0.106 - 0.212: 779 0.212 - 0.318: 116 0.318 - 0.425: 27 0.425 - 0.531: 9 Chirality restraints: 3615 Sorted by residual: chirality pdb=" CB VAL A 826 " pdb=" CA VAL A 826 " pdb=" CG1 VAL A 826 " pdb=" CG2 VAL A 826 " both_signs ideal model delta sigma weight residual False -2.63 -3.16 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CB ILE C 850 " pdb=" CA ILE C 850 " pdb=" CG1 ILE C 850 " pdb=" CG2 ILE C 850 " both_signs ideal model delta sigma weight residual False 2.64 3.15 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C2 NAG B1304 " pdb=" C1 NAG B1304 " pdb=" C3 NAG B1304 " pdb=" N2 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.49 -2.97 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 3612 not shown) Planarity restraints: 4072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 717 " -0.066 2.00e-02 2.50e+03 6.97e-02 6.08e+01 pdb=" CG ASN C 717 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 717 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 717 " 0.109 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " -0.043 2.00e-02 2.50e+03 4.60e-02 2.64e+01 pdb=" CG ASN B 717 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " 0.073 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " -0.066 2.00e-02 2.50e+03 3.61e-02 2.61e+01 pdb=" CG TYR B 904 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " -0.057 2.00e-02 2.50e+03 ... (remaining 4069 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 926 2.67 - 3.23: 21380 3.23 - 3.79: 36890 3.79 - 4.34: 49490 4.34 - 4.90: 80169 Nonbonded interactions: 188855 Sorted by model distance: nonbonded pdb=" ND2 ASN L 27 " pdb=" OE1 GLN L 31 " model vdw 2.116 3.120 nonbonded pdb=" O VAL L 28 " pdb=" N GLN L 31 " model vdw 2.320 3.120 nonbonded pdb=" N PRO L 7 " pdb=" O PRO L 7 " model vdw 2.329 2.496 nonbonded pdb=" N ASP L 26 " pdb=" N ASN L 27 " model vdw 2.357 2.560 nonbonded pdb=" C VAL L 28 " pdb=" N SER L 30 " model vdw 2.361 3.350 ... (remaining 188850 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 'B' and (resid 28 through 1144 or resid 1302 through 1304)) selection = (chain 'C' and (resid 28 through 143 or resid 154 through 331 or resid 531 throu \ gh 827 or resid 854 through 1144 or resid 1301 through 1303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.880 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.900 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.022 0.340 23103 Z= 1.145 Angle : 1.791 14.319 31467 Z= 1.221 Chirality : 0.103 0.531 3615 Planarity : 0.008 0.055 4061 Dihedral : 9.883 88.565 8447 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.08 % Allowed : 0.67 % Favored : 99.25 % 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: 0.76 (0.14), residues: 2822 helix: 0.73 (0.18), residues: 621 sheet: 1.28 (0.19), residues: 657 loop : 0.16 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1000 TYR 0.066 0.008 TYR B 904 PHE 0.046 0.006 PHE A 888 TRP 0.040 0.010 TRP H 36 HIS 0.011 0.002 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.02119 (23056) covalent geometry : angle 1.78784 (31362) SS BOND : bond 0.09002 ( 36) SS BOND : angle 2.51113 ( 72) hydrogen bonds : bond 0.15925 ( 1037) hydrogen bonds : angle 8.19102 ( 2913) link_NAG-ASN : bond 0.08749 ( 11) link_NAG-ASN : angle 2.48109 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 582 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 TRP cc_start: 0.6830 (t60) cc_final: 0.6528 (t60) REVERT: C 98 SER cc_start: 0.6900 (m) cc_final: 0.6460 (t) REVERT: C 128 ILE cc_start: 0.7390 (mt) cc_final: 0.6909 (tt) REVERT: C 229 LEU cc_start: 0.7140 (mt) cc_final: 0.6783 (mt) REVERT: C 589 PRO cc_start: 0.7976 (Cg_exo) cc_final: 0.7733 (Cg_endo) REVERT: C 756 TYR cc_start: 0.5727 (m-80) cc_final: 0.5472 (m-80) REVERT: C 869 MET cc_start: 0.8576 (mtt) cc_final: 0.8369 (mtt) REVERT: C 973 ILE cc_start: 0.7142 (pt) cc_final: 0.6817 (mt) REVERT: C 1029 MET cc_start: 0.8808 (tpp) cc_final: 0.8444 (tpp) REVERT: A 234 ASN cc_start: 0.5550 (m-40) cc_final: 0.4979 (t0) REVERT: A 353 TRP cc_start: 0.5018 (m-90) cc_final: 0.4532 (m-90) REVERT: A 453 TYR cc_start: 0.6929 (p90) cc_final: 0.6717 (p90) REVERT: A 495 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6379 (p90) REVERT: A 756 TYR cc_start: 0.4976 (m-80) cc_final: 0.4730 (m-80) REVERT: A 761 THR cc_start: 0.8098 (m) cc_final: 0.7804 (t) REVERT: A 762 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7428 (mm-40) REVERT: A 1138 TYR cc_start: 0.6540 (m-80) cc_final: 0.6226 (t80) REVERT: B 129 LYS cc_start: 0.8021 (mttt) cc_final: 0.7533 (tttt) REVERT: B 227 VAL cc_start: 0.8603 (p) cc_final: 0.8370 (t) REVERT: B 241 LEU cc_start: 0.7665 (mt) cc_final: 0.7158 (mt) REVERT: B 823 PHE cc_start: 0.7154 (m-80) cc_final: 0.6953 (m-80) REVERT: H 34 MET cc_start: 0.7258 (mmm) cc_final: 0.6809 (tpp) REVERT: H 95 ASP cc_start: 0.5856 (t0) cc_final: 0.4949 (t0) outliers start: 2 outliers final: 1 residues processed: 584 average time/residue: 0.1758 time to fit residues: 152.1826 Evaluate side-chains 243 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 271 GLN C 762 GLN C1054 GLN C1113 GLN C1135 ASN A 49 HIS A 121 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 762 GLN A 804 GLN A 914 ASN A1048 HIS B 115 GLN B 188 ASN B 239 GLN B 949 GLN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.108705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087654 restraints weight = 56163.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088737 restraints weight = 45023.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089073 restraints weight = 33138.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.089434 restraints weight = 29612.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.089450 restraints weight = 28004.724| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 23103 Z= 0.208 Angle : 0.744 8.294 31467 Z= 0.405 Chirality : 0.049 0.193 3615 Planarity : 0.005 0.048 4061 Dihedral : 5.700 31.781 3294 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 2.26 % Allowed : 7.53 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.81 (0.15), residues: 2822 helix: 2.24 (0.20), residues: 615 sheet: 0.93 (0.19), residues: 684 loop : -0.35 (0.14), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 577 TYR 0.028 0.002 TYR A 505 PHE 0.044 0.002 PHE A 888 TRP 0.017 0.002 TRP A 64 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00472 (23056) covalent geometry : angle 0.73535 (31362) SS BOND : bond 0.00517 ( 36) SS BOND : angle 2.00424 ( 72) hydrogen bonds : bond 0.05889 ( 1037) hydrogen bonds : angle 6.58818 ( 2913) link_NAG-ASN : bond 0.00508 ( 11) link_NAG-ASN : angle 2.21316 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 322 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6736 (m) cc_final: 0.6340 (t) REVERT: C 153 MET cc_start: 0.2529 (ttt) cc_final: 0.2069 (mtt) REVERT: C 973 ILE cc_start: 0.7092 (pt) cc_final: 0.6679 (mt) REVERT: C 1138 TYR cc_start: 0.6916 (t80) cc_final: 0.6667 (t80) REVERT: A 228 ASP cc_start: 0.6707 (m-30) cc_final: 0.5923 (p0) REVERT: A 234 ASN cc_start: 0.5282 (m-40) cc_final: 0.4934 (t0) REVERT: A 650 LEU cc_start: 0.8756 (tp) cc_final: 0.8536 (tt) REVERT: A 752 LEU cc_start: 0.7475 (mt) cc_final: 0.7022 (tp) REVERT: A 761 THR cc_start: 0.8270 (m) cc_final: 0.8003 (t) REVERT: A 762 GLN cc_start: 0.7851 (mm110) cc_final: 0.7441 (mm-40) REVERT: B 129 LYS cc_start: 0.7884 (mttt) cc_final: 0.7387 (tttt) REVERT: B 218 GLN cc_start: 0.7175 (mt0) cc_final: 0.6474 (mp10) REVERT: B 651 ILE cc_start: 0.8550 (mm) cc_final: 0.8260 (mt) REVERT: B 957 GLN cc_start: 0.7167 (mt0) cc_final: 0.6939 (mm-40) REVERT: B 983 ARG cc_start: 0.6795 (mpt180) cc_final: 0.6555 (mmt-90) REVERT: B 985 ASP cc_start: 0.6698 (p0) cc_final: 0.5320 (p0) REVERT: H 58 PHE cc_start: 0.7064 (m-80) cc_final: 0.6149 (m-10) REVERT: H 85 ASP cc_start: 0.6863 (m-30) cc_final: 0.6646 (t0) REVERT: H 108 LEU cc_start: 0.6114 (tt) cc_final: 0.5847 (tp) outliers start: 57 outliers final: 34 residues processed: 357 average time/residue: 0.1399 time to fit residues: 80.4248 Evaluate side-chains 248 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 147 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 233 optimal weight: 0.0980 chunk 143 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 87 ASN A 121 ASN A 321 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 675 GLN A 992 GLN B 188 ASN B 207 HIS B 969 ASN B1048 HIS ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.106462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.085855 restraints weight = 56484.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.086486 restraints weight = 49035.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.086933 restraints weight = 38260.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.087210 restraints weight = 32520.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.087254 restraints weight = 30942.676| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 23103 Z= 0.204 Angle : 0.676 7.986 31467 Z= 0.363 Chirality : 0.047 0.215 3615 Planarity : 0.004 0.040 4061 Dihedral : 5.479 35.072 3292 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.55 % Favored : 97.41 % Rotamer: Outliers : 2.97 % Allowed : 9.27 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.60 (0.15), residues: 2822 helix: 2.41 (0.20), residues: 601 sheet: 0.76 (0.18), residues: 685 loop : -0.60 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1107 TYR 0.027 0.002 TYR C1067 PHE 0.031 0.002 PHE A 888 TRP 0.016 0.002 TRP A 64 HIS 0.007 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00470 (23056) covalent geometry : angle 0.66708 (31362) SS BOND : bond 0.00536 ( 36) SS BOND : angle 1.85378 ( 72) hydrogen bonds : bond 0.05096 ( 1037) hydrogen bonds : angle 6.24389 ( 2913) link_NAG-ASN : bond 0.00371 ( 11) link_NAG-ASN : angle 2.22587 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 244 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 ASN cc_start: 0.4030 (m-40) cc_final: 0.3257 (m110) REVERT: C 98 SER cc_start: 0.6506 (m) cc_final: 0.6127 (t) REVERT: C 238 PHE cc_start: 0.6116 (OUTLIER) cc_final: 0.5363 (t80) REVERT: C 614 ASP cc_start: 0.6987 (t0) cc_final: 0.6775 (t0) REVERT: C 1113 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6545 (mp-120) REVERT: A 153 MET cc_start: 0.1208 (pmm) cc_final: 0.0343 (ppp) REVERT: A 228 ASP cc_start: 0.6843 (m-30) cc_final: 0.5888 (p0) REVERT: A 234 ASN cc_start: 0.5307 (m-40) cc_final: 0.4973 (t0) REVERT: A 650 LEU cc_start: 0.8643 (tp) cc_final: 0.8376 (tt) REVERT: A 869 MET cc_start: 0.7937 (mtm) cc_final: 0.7736 (mtm) REVERT: B 129 LYS cc_start: 0.8068 (mttt) cc_final: 0.7611 (mttm) REVERT: B 218 GLN cc_start: 0.7033 (mt0) cc_final: 0.6480 (mp10) REVERT: B 957 GLN cc_start: 0.7132 (mt0) cc_final: 0.6932 (mm-40) REVERT: H 85 ASP cc_start: 0.6861 (m-30) cc_final: 0.6593 (t0) outliers start: 75 outliers final: 56 residues processed: 299 average time/residue: 0.1342 time to fit residues: 65.8129 Evaluate side-chains 258 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 110 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 205 optimal weight: 0.6980 chunk 251 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 856 ASN C1088 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.106742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.086581 restraints weight = 56285.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.086915 restraints weight = 49850.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.087246 restraints weight = 40469.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.087538 restraints weight = 35625.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087905 restraints weight = 34042.028| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23103 Z= 0.161 Angle : 0.611 7.222 31467 Z= 0.328 Chirality : 0.046 0.233 3615 Planarity : 0.004 0.039 4061 Dihedral : 5.241 34.707 3292 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.08 % Favored : 96.88 % Rotamer: Outliers : 3.05 % Allowed : 10.34 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.53 (0.15), residues: 2822 helix: 2.53 (0.20), residues: 609 sheet: 0.74 (0.19), residues: 665 loop : -0.75 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.023 0.002 TYR C1067 PHE 0.021 0.002 PHE B 888 TRP 0.018 0.002 TRP A 64 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00367 (23056) covalent geometry : angle 0.60350 (31362) SS BOND : bond 0.00469 ( 36) SS BOND : angle 1.56537 ( 72) hydrogen bonds : bond 0.04580 ( 1037) hydrogen bonds : angle 5.99327 ( 2913) link_NAG-ASN : bond 0.00302 ( 11) link_NAG-ASN : angle 2.09119 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 229 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: C 87 ASN cc_start: 0.3811 (m-40) cc_final: 0.3500 (m110) REVERT: C 98 SER cc_start: 0.6425 (m) cc_final: 0.6184 (t) REVERT: C 238 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5256 (t80) REVERT: C 614 ASP cc_start: 0.6936 (t0) cc_final: 0.6470 (t0) REVERT: C 1113 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6491 (mp-120) REVERT: A 64 TRP cc_start: 0.5733 (t-100) cc_final: 0.5453 (t-100) REVERT: A 153 MET cc_start: 0.1349 (pmm) cc_final: 0.0399 (ppp) REVERT: A 500 THR cc_start: 0.7024 (OUTLIER) cc_final: 0.6690 (t) REVERT: B 129 LYS cc_start: 0.8085 (mttt) cc_final: 0.7828 (mttt) REVERT: B 218 GLN cc_start: 0.7224 (mt0) cc_final: 0.6459 (mp10) REVERT: B 651 ILE cc_start: 0.8558 (mm) cc_final: 0.8193 (mt) REVERT: H 78 LEU cc_start: 0.6590 (tp) cc_final: 0.6297 (mt) REVERT: H 108 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.5630 (tp) outliers start: 77 outliers final: 57 residues processed: 283 average time/residue: 0.1346 time to fit residues: 62.6349 Evaluate side-chains 257 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 66 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 273 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 259 optimal weight: 0.6980 chunk 76 optimal weight: 0.0870 chunk 274 optimal weight: 5.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 856 ASN A 66 HIS A 388 ASN B 207 HIS B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.106216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.086050 restraints weight = 55987.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.086793 restraints weight = 51405.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086984 restraints weight = 41989.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.087313 restraints weight = 36029.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.087407 restraints weight = 33650.762| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23103 Z= 0.166 Angle : 0.601 7.409 31467 Z= 0.322 Chirality : 0.046 0.179 3615 Planarity : 0.004 0.040 4061 Dihedral : 5.140 34.258 3292 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 3.45 % Allowed : 10.54 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.40 (0.15), residues: 2822 helix: 2.52 (0.20), residues: 610 sheet: 0.64 (0.19), residues: 680 loop : -0.88 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 765 TYR 0.023 0.002 TYR C1067 PHE 0.021 0.002 PHE B 888 TRP 0.018 0.002 TRP A 64 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00382 (23056) covalent geometry : angle 0.59421 (31362) SS BOND : bond 0.00519 ( 36) SS BOND : angle 1.50604 ( 72) hydrogen bonds : bond 0.04477 ( 1037) hydrogen bonds : angle 5.89011 ( 2913) link_NAG-ASN : bond 0.00320 ( 11) link_NAG-ASN : angle 2.05635 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 218 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6362 (m) cc_final: 0.6139 (t) REVERT: C 238 PHE cc_start: 0.6224 (OUTLIER) cc_final: 0.5267 (t80) REVERT: C 983 ARG cc_start: 0.6454 (mtm-85) cc_final: 0.6173 (mtm180) REVERT: C 1113 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6516 (mp-120) REVERT: A 64 TRP cc_start: 0.5561 (OUTLIER) cc_final: 0.5072 (t60) REVERT: A 136 CYS cc_start: 0.5278 (OUTLIER) cc_final: 0.4578 (t) REVERT: A 153 MET cc_start: 0.1697 (pmm) cc_final: 0.0725 (ppp) REVERT: A 228 ASP cc_start: 0.6076 (OUTLIER) cc_final: 0.5614 (m-30) REVERT: A 500 THR cc_start: 0.7148 (OUTLIER) cc_final: 0.6841 (t) REVERT: B 129 LYS cc_start: 0.8107 (mttt) cc_final: 0.7834 (mttt) REVERT: B 218 GLN cc_start: 0.7330 (mt0) cc_final: 0.6456 (mp10) REVERT: B 651 ILE cc_start: 0.8583 (mm) cc_final: 0.8235 (mt) REVERT: H 58 PHE cc_start: 0.6918 (m-80) cc_final: 0.6700 (m-80) REVERT: H 82 ASN cc_start: 0.7782 (t0) cc_final: 0.7575 (m-40) outliers start: 87 outliers final: 61 residues processed: 283 average time/residue: 0.1329 time to fit residues: 62.5765 Evaluate side-chains 263 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 196 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 202 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 203 optimal weight: 0.0970 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1064 HIS B 271 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.105088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.085530 restraints weight = 56679.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.085392 restraints weight = 50012.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.085788 restraints weight = 48607.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.086094 restraints weight = 38785.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086261 restraints weight = 35440.766| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23103 Z= 0.213 Angle : 0.640 9.620 31467 Z= 0.341 Chirality : 0.047 0.187 3615 Planarity : 0.005 0.065 4061 Dihedral : 5.299 33.453 3291 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 3.45 % Allowed : 11.49 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.27 (0.15), residues: 2822 helix: 2.35 (0.20), residues: 616 sheet: 0.52 (0.19), residues: 696 loop : -0.95 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.025 0.002 TYR C1067 PHE 0.036 0.002 PHE A 133 TRP 0.019 0.002 TRP A 64 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00497 (23056) covalent geometry : angle 0.63232 (31362) SS BOND : bond 0.00527 ( 36) SS BOND : angle 1.57996 ( 72) hydrogen bonds : bond 0.04668 ( 1037) hydrogen bonds : angle 5.94748 ( 2913) link_NAG-ASN : bond 0.00351 ( 11) link_NAG-ASN : angle 2.26848 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 213 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6290 (m) cc_final: 0.6084 (t) REVERT: C 130 VAL cc_start: 0.6443 (OUTLIER) cc_final: 0.6211 (p) REVERT: C 173 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6700 (pm20) REVERT: C 238 PHE cc_start: 0.6256 (OUTLIER) cc_final: 0.5378 (t80) REVERT: C 614 ASP cc_start: 0.6891 (t0) cc_final: 0.6483 (t0) REVERT: C 1113 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6586 (mp-120) REVERT: C 1127 ASP cc_start: 0.6406 (m-30) cc_final: 0.5856 (p0) REVERT: A 64 TRP cc_start: 0.5667 (OUTLIER) cc_final: 0.5338 (t60) REVERT: A 153 MET cc_start: 0.1963 (pmm) cc_final: 0.0954 (ppp) REVERT: A 228 ASP cc_start: 0.6024 (OUTLIER) cc_final: 0.5554 (m-30) REVERT: A 500 THR cc_start: 0.7096 (OUTLIER) cc_final: 0.6843 (t) REVERT: B 218 GLN cc_start: 0.7245 (mt0) cc_final: 0.6930 (mt0) REVERT: B 1019 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7836 (ttm110) REVERT: H 58 PHE cc_start: 0.6992 (m-80) cc_final: 0.6632 (m-80) REVERT: H 82 ASN cc_start: 0.7913 (t0) cc_final: 0.7691 (m-40) outliers start: 87 outliers final: 67 residues processed: 282 average time/residue: 0.1370 time to fit residues: 63.3851 Evaluate side-chains 267 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 193 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 98 optimal weight: 0.3980 chunk 89 optimal weight: 9.9990 chunk 220 optimal weight: 0.4980 chunk 257 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 204 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1054 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.106901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087431 restraints weight = 56215.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.087546 restraints weight = 48683.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.088042 restraints weight = 45314.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.088301 restraints weight = 36200.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088418 restraints weight = 33360.472| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23103 Z= 0.118 Angle : 0.565 10.930 31467 Z= 0.301 Chirality : 0.044 0.169 3615 Planarity : 0.004 0.042 4061 Dihedral : 4.952 33.944 3291 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 2.85 % Allowed : 12.80 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.45 (0.15), residues: 2822 helix: 2.81 (0.20), residues: 597 sheet: 0.55 (0.19), residues: 675 loop : -0.86 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.020 0.001 TYR C1067 PHE 0.019 0.001 PHE B 888 TRP 0.017 0.002 TRP A 353 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00260 (23056) covalent geometry : angle 0.55778 (31362) SS BOND : bond 0.00285 ( 36) SS BOND : angle 1.49121 ( 72) hydrogen bonds : bond 0.04111 ( 1037) hydrogen bonds : angle 5.73475 ( 2913) link_NAG-ASN : bond 0.00260 ( 11) link_NAG-ASN : angle 1.92241 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 229 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5430 (t80) REVERT: C 1113 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6523 (mp-120) REVERT: C 1127 ASP cc_start: 0.6393 (m-30) cc_final: 0.5923 (p0) REVERT: A 64 TRP cc_start: 0.5545 (OUTLIER) cc_final: 0.5331 (t60) REVERT: A 153 MET cc_start: 0.1695 (pmm) cc_final: 0.0716 (ppp) REVERT: B 218 GLN cc_start: 0.7164 (mt0) cc_final: 0.6625 (mt0) REVERT: B 651 ILE cc_start: 0.8550 (mm) cc_final: 0.8210 (mt) REVERT: B 1019 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7978 (ttp-170) REVERT: L 73 LEU cc_start: 0.6717 (tp) cc_final: 0.6392 (tt) outliers start: 72 outliers final: 57 residues processed: 279 average time/residue: 0.1341 time to fit residues: 61.6764 Evaluate side-chains 265 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 18 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 142 optimal weight: 0.0470 chunk 116 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.107297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.087695 restraints weight = 56158.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087769 restraints weight = 48563.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.088197 restraints weight = 47892.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.088477 restraints weight = 36670.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088611 restraints weight = 33461.922| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23103 Z= 0.117 Angle : 0.556 9.500 31467 Z= 0.296 Chirality : 0.044 0.172 3615 Planarity : 0.004 0.043 4061 Dihedral : 4.789 32.701 3291 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 2.69 % Allowed : 13.43 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.45 (0.15), residues: 2822 helix: 2.79 (0.20), residues: 611 sheet: 0.54 (0.19), residues: 673 loop : -0.89 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 983 TYR 0.019 0.001 TYR C1067 PHE 0.024 0.001 PHE C 186 TRP 0.017 0.002 TRP A 353 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00262 (23056) covalent geometry : angle 0.55032 (31362) SS BOND : bond 0.00268 ( 36) SS BOND : angle 1.38129 ( 72) hydrogen bonds : bond 0.03976 ( 1037) hydrogen bonds : angle 5.63934 ( 2913) link_NAG-ASN : bond 0.00259 ( 11) link_NAG-ASN : angle 1.78432 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 223 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 PHE cc_start: 0.6190 (OUTLIER) cc_final: 0.5408 (t80) REVERT: C 1113 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6543 (mp-120) REVERT: C 1127 ASP cc_start: 0.6298 (m-30) cc_final: 0.5864 (p0) REVERT: A 153 MET cc_start: 0.1705 (pmm) cc_final: 0.0741 (ppp) REVERT: B 168 PHE cc_start: 0.6644 (p90) cc_final: 0.6135 (p90) REVERT: B 651 ILE cc_start: 0.8498 (mm) cc_final: 0.8153 (mt) REVERT: B 1019 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8002 (ttp-170) REVERT: B 1092 GLU cc_start: 0.6936 (pp20) cc_final: 0.6665 (pp20) REVERT: L 73 LEU cc_start: 0.6664 (tp) cc_final: 0.6379 (tt) outliers start: 68 outliers final: 53 residues processed: 269 average time/residue: 0.1362 time to fit residues: 60.1238 Evaluate side-chains 261 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 280 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1142 GLN A 394 ASN A 856 ASN B 957 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.105702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.085997 restraints weight = 56553.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.085728 restraints weight = 50502.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086122 restraints weight = 47910.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086457 restraints weight = 39414.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.086622 restraints weight = 35673.136| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 23103 Z= 0.176 Angle : 0.607 9.053 31467 Z= 0.323 Chirality : 0.045 0.177 3615 Planarity : 0.004 0.042 4061 Dihedral : 4.963 32.394 3291 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 2.89 % Allowed : 13.31 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.31 (0.15), residues: 2822 helix: 2.62 (0.20), residues: 615 sheet: 0.39 (0.19), residues: 700 loop : -0.95 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 983 TYR 0.023 0.002 TYR C1067 PHE 0.021 0.002 PHE B 888 TRP 0.020 0.002 TRP A 64 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00407 (23056) covalent geometry : angle 0.59709 (31362) SS BOND : bond 0.00417 ( 36) SS BOND : angle 1.99686 ( 72) hydrogen bonds : bond 0.04302 ( 1037) hydrogen bonds : angle 5.75179 ( 2913) link_NAG-ASN : bond 0.00314 ( 11) link_NAG-ASN : angle 2.03065 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 205 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: C 173 GLN cc_start: 0.6032 (mp10) cc_final: 0.5812 (mp10) REVERT: C 238 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5472 (t80) REVERT: C 983 ARG cc_start: 0.6891 (ttm110) cc_final: 0.6339 (mtm110) REVERT: C 1113 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6591 (mp-120) REVERT: C 1127 ASP cc_start: 0.6482 (m-30) cc_final: 0.5961 (p0) REVERT: A 153 MET cc_start: 0.1763 (pmm) cc_final: 0.0820 (ppp) REVERT: A 228 ASP cc_start: 0.6005 (OUTLIER) cc_final: 0.5558 (m-30) REVERT: B 855 PHE cc_start: 0.6550 (m-80) cc_final: 0.6344 (m-80) REVERT: B 1019 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8049 (ttp-170) REVERT: B 1092 GLU cc_start: 0.7130 (pp20) cc_final: 0.6683 (pp20) outliers start: 73 outliers final: 59 residues processed: 259 average time/residue: 0.1332 time to fit residues: 57.3991 Evaluate side-chains 261 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 269 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 278 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 266 optimal weight: 9.9990 chunk 155 optimal weight: 0.0020 chunk 139 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 992 GLN B1002 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.107583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.088118 restraints weight = 56366.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087802 restraints weight = 49135.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.088335 restraints weight = 46951.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088532 restraints weight = 39651.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088706 restraints weight = 37365.221| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23103 Z= 0.113 Angle : 0.567 11.212 31467 Z= 0.299 Chirality : 0.044 0.179 3615 Planarity : 0.004 0.044 4061 Dihedral : 4.736 31.819 3291 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 2.10 % Allowed : 14.22 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.43 (0.15), residues: 2822 helix: 2.80 (0.20), residues: 613 sheet: 0.44 (0.19), residues: 702 loop : -0.89 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 983 TYR 0.020 0.001 TYR C1067 PHE 0.016 0.001 PHE B 592 TRP 0.021 0.002 TRP A 353 HIS 0.005 0.000 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00252 (23056) covalent geometry : angle 0.55937 (31362) SS BOND : bond 0.00266 ( 36) SS BOND : angle 1.71896 ( 72) hydrogen bonds : bond 0.03873 ( 1037) hydrogen bonds : angle 5.58109 ( 2913) link_NAG-ASN : bond 0.00227 ( 11) link_NAG-ASN : angle 1.73305 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.1780 (ttt) cc_final: 0.1388 (mtt) REVERT: C 173 GLN cc_start: 0.5975 (mp10) cc_final: 0.5730 (mp10) REVERT: C 238 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5543 (t80) REVERT: C 1113 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6568 (mp-120) REVERT: C 1127 ASP cc_start: 0.6444 (m-30) cc_final: 0.6013 (p0) REVERT: A 153 MET cc_start: 0.1664 (pmm) cc_final: 0.0699 (ppp) REVERT: A 675 GLN cc_start: 0.5488 (OUTLIER) cc_final: 0.5168 (pp30) REVERT: A 1129 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7645 (p) REVERT: B 651 ILE cc_start: 0.8510 (mm) cc_final: 0.8184 (mt) REVERT: B 1019 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7986 (ttp-170) REVERT: B 1092 GLU cc_start: 0.7065 (pp20) cc_final: 0.6653 (pp20) outliers start: 53 outliers final: 42 residues processed: 257 average time/residue: 0.1435 time to fit residues: 60.2032 Evaluate side-chains 248 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 125 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 33 optimal weight: 0.1980 chunk 239 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** H 32 ASN ** 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 = 0.3606 r_free = 0.3606 target = 0.107516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.087890 restraints weight = 56037.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087929 restraints weight = 47610.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088411 restraints weight = 42165.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088658 restraints weight = 36917.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.088745 restraints weight = 34312.356| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23103 Z= 0.117 Angle : 0.570 9.535 31467 Z= 0.301 Chirality : 0.045 0.228 3615 Planarity : 0.004 0.043 4061 Dihedral : 4.639 31.948 3291 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 1.94 % Allowed : 14.82 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.42 (0.15), residues: 2822 helix: 2.82 (0.20), residues: 613 sheet: 0.40 (0.19), residues: 706 loop : -0.90 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.020 0.001 TYR C1067 PHE 0.016 0.001 PHE B 592 TRP 0.023 0.002 TRP A 64 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00261 (23056) covalent geometry : angle 0.56343 (31362) SS BOND : bond 0.00304 ( 36) SS BOND : angle 1.51297 ( 72) hydrogen bonds : bond 0.03863 ( 1037) hydrogen bonds : angle 5.51918 ( 2913) link_NAG-ASN : bond 0.00238 ( 11) link_NAG-ASN : angle 1.70099 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3388.95 seconds wall clock time: 59 minutes 30.56 seconds (3570.56 seconds total)