Starting phenix.real_space_refine on Mon Aug 25 14:23:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k9b_36983/08_2025/8k9b_36983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9b_36983/08_2025/8k9b_36983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k9b_36983/08_2025/8k9b_36983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9b_36983/08_2025/8k9b_36983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k9b_36983/08_2025/8k9b_36983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9b_36983/08_2025/8k9b_36983.map" } resolution = 4.5 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= 0.009 sd= 0.093 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 130 5.16 5 C 18105 2.51 5 N 4744 2.21 5 O 5461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28440 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 8407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8407 Classifications: {'peptide': 1075} Link IDs: {'CIS': 2, 'PTRANS': 53, 'TRANS': 1019} Chain breaks: 4 Chain: "A" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1633 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 201} Chain: "B" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1699 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain: "C" Number of atoms: 8332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8332 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 52, 'TRANS': 1012} Chain breaks: 5 Chain: "D" Number of atoms: 8355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8355 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 5 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.88, per 1000 atoms: 0.21 Number of scatterers: 28440 At special positions: 0 Unit cell: (184.62, 184.62, 192.78, 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 130 16.00 O 5461 8.00 N 4744 7.00 C 18105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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 E1301 " - " ASN E 122 " Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6818 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 57 sheets defined 21.7% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 388 removed outlier: 3.610A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 removed outlier: 4.439A pdb=" N ARG E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 737 through 744 removed outlier: 3.778A pdb=" N ILE E 742 " --> pdb=" O CYS E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 757 Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 825 removed outlier: 3.899A pdb=" N LEU E 821 " --> pdb=" O PHE E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 856 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 913 through 941 removed outlier: 3.688A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN E 925 " --> pdb=" O LYS E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 968 removed outlier: 3.580A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU E 966 " --> pdb=" O LEU E 962 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 968 " --> pdb=" O LYS E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1032 Processing helix chain 'E' and resid 1116 through 1118 No H-bonds generated for 'chain 'E' and resid 1116 through 1118' Processing helix chain 'E' and resid 1140 through 1145 removed outlier: 4.040A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.948A pdb=" N LEU B 88 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.677A pdb=" N HIS B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.666A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.650A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.521A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.517A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.505A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) 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 removed outlier: 3.587A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 365 through 371 removed outlier: 4.236A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.531A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 758 through 783 Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 849 through 856 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.730A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.522A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.624A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.625A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 Processing helix chain 'D' and resid 1116 through 1118 No H-bonds generated for 'chain 'D' and resid 1116 through 1118' Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 4.245A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 30 removed outlier: 4.252A pdb=" N ALA E 27 " --> pdb=" O TRP E 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA E 264 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 195 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.601A pdb=" N VAL E 289 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.923A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS E 131 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 156 through 157 removed outlier: 3.671A pdb=" N GLU E 156 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY E 142 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU E 141 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 244 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR E 259 " --> pdb=" O HIS E 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.600A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER E 596 " --> pdb=" O LEU E 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 325 through 328 Processing sheet with id=AA7, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.055A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR E 508 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 435 " --> pdb=" O THR E 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.678A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 654 through 660 removed outlier: 4.356A pdb=" N THR E 696 " --> pdb=" O VAL E 656 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN E 658 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'E' and resid 711 through 728 removed outlier: 3.661A pdb=" N ILE E 714 " --> pdb=" O LYS E1073 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS E1073 " --> pdb=" O ILE E 714 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 711 through 728 removed outlier: 3.661A pdb=" N ILE E 714 " --> pdb=" O LYS E1073 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS E1073 " --> pdb=" O ILE E 714 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'E' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.653A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 5 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.830A pdb=" N MET A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TRP A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRP A 36 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 59 " --> pdb=" O TRP A 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.752A pdb=" N GLY A 98 " --> pdb=" O TYR A 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 108 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 126 through 130 removed outlier: 3.523A pdb=" N LYS A 149 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 145 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 150 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR A 181 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 126 through 130 removed outlier: 3.523A pdb=" N LYS A 149 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 145 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 150 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR A 181 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 157 through 160 removed outlier: 4.801A pdb=" N VAL A 199 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 214 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.596A pdb=" N SER B 22 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 19 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.584A pdb=" N GLU B 110 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY B 89 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP B 40 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.390A pdb=" N TYR B 178 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER B 181 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 167 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 158 through 159 removed outlier: 6.317A pdb=" N HIS B 203 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER B 208 " --> pdb=" O HIS B 203 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.986A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.690A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.666A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.666A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.573A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.980A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.399A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.612A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.912A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 701 through 704 removed outlier: 3.545A pdb=" N LYS D 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.853A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'D' and resid 28 through 31 removed outlier: 4.059A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.673A pdb=" N VAL D 289 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 83 through 85 removed outlier: 3.884A pdb=" N LEU D 141 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 244 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 246 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 83 through 85 removed outlier: 5.906A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 311 through 317 removed outlier: 3.534A pdb=" N GLY D 311 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 315 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 325 through 328 removed outlier: 4.980A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.864A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE D 402 " --> pdb=" O TYR D 508 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.834A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF7, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF8, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.989A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 711 through 728 removed outlier: 3.606A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 711 through 728 removed outlier: 3.606A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN D1071 " --> pdb=" O THR D 716 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 718 " --> pdb=" O PRO D1069 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE D 720 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR D1067 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 722 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL D1065 " --> pdb=" O VAL D 722 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR D 724 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU D1063 " --> pdb=" O THR D 724 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 726 " --> pdb=" O VAL D1061 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL D1061 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY D1059 " --> pdb=" O PRO D 728 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.025A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 1120 through 1122 1109 hydrogen bonds defined for protein. 3072 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: 6.33 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9208 1.34 - 1.46: 7103 1.46 - 1.58: 12625 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 29101 Sorted by residual: bond pdb=" C1 NAG E1301 " pdb=" O5 NAG E1301 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" N ASP B 1 " pdb=" CA ASP B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N GLN E 14 " pdb=" CA GLN E 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N GLN D 14 " pdb=" CA GLN D 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N GLU A 1 " pdb=" CA GLU A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 ... (remaining 29096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 38641 1.10 - 2.20: 721 2.20 - 3.29: 160 3.29 - 4.39: 76 4.39 - 5.49: 8 Bond angle restraints: 39606 Sorted by residual: angle pdb=" C ARG C 21 " pdb=" CA ARG C 21 " pdb=" CB ARG C 21 " ideal model delta sigma weight residual 115.79 111.09 4.70 1.19e+00 7.06e-01 1.56e+01 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 111.56 108.31 3.25 8.60e-01 1.35e+00 1.43e+01 angle pdb=" N ILE C 666 " pdb=" CA ILE C 666 " pdb=" C ILE C 666 " ideal model delta sigma weight residual 111.62 108.82 2.80 7.90e-01 1.60e+00 1.25e+01 angle pdb=" N ILE E 666 " pdb=" CA ILE E 666 " pdb=" C ILE E 666 " ideal model delta sigma weight residual 111.56 108.59 2.97 8.60e-01 1.35e+00 1.19e+01 angle pdb=" N VAL D 341 " pdb=" CA VAL D 341 " pdb=" C VAL D 341 " ideal model delta sigma weight residual 111.62 109.02 2.60 7.90e-01 1.60e+00 1.09e+01 ... (remaining 39601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 16857 16.94 - 33.87: 391 33.87 - 50.81: 93 50.81 - 67.75: 25 67.75 - 84.68: 8 Dihedral angle restraints: 17374 sinusoidal: 6773 harmonic: 10601 Sorted by residual: dihedral pdb=" CA ASN E 148 " pdb=" C ASN E 148 " pdb=" N ASN E 149 " pdb=" CA ASN E 149 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CB CYS A 146 " pdb=" SG CYS A 146 " pdb=" SG CYS A 201 " pdb=" CB CYS A 201 " ideal model delta sinusoidal sigma weight residual 93.00 53.93 39.07 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 61.12 31.88 1 1.00e+01 1.00e-02 1.45e+01 ... (remaining 17371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2835 0.029 - 0.057: 1110 0.057 - 0.086: 138 0.086 - 0.115: 302 0.115 - 0.143: 97 Chirality restraints: 4482 Sorted by residual: chirality pdb=" CA ILE E 714 " pdb=" N ILE E 714 " pdb=" C ILE E 714 " pdb=" CB ILE E 714 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE D 714 " pdb=" N ILE D 714 " pdb=" C ILE D 714 " pdb=" CB ILE D 714 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE C 664 " pdb=" N ILE C 664 " pdb=" C ILE C 664 " pdb=" CB ILE C 664 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 4479 not shown) Planarity restraints: 5139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 916 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C LEU E 916 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU E 916 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR E 917 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 986 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO E 987 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 987 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 987 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 61 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 62 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " 0.017 5.00e-02 4.00e+02 ... (remaining 5136 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 195 2.57 - 3.16: 23448 3.16 - 3.74: 42621 3.74 - 4.32: 60796 4.32 - 4.90: 102793 Nonbonded interactions: 229853 Sorted by model distance: nonbonded pdb=" OH TYR D 756 " pdb=" OD1 ASP D 994 " model vdw 1.993 3.040 nonbonded pdb=" OH TYR E 756 " pdb=" OD1 ASP E 994 " model vdw 1.999 3.040 nonbonded pdb=" OG SER C 383 " pdb=" OD1 ASP D 985 " model vdw 2.012 3.040 nonbonded pdb=" OD1 ASP E 985 " pdb=" OG SER D 383 " model vdw 2.014 3.040 nonbonded pdb=" OG SER E 813 " pdb=" OE1 GLU E 868 " model vdw 2.024 3.040 ... (remaining 229848 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 'C' selection = (chain 'D' and (resid 16 through 827 or resid 849 through 1147)) selection = (chain 'E' and (resid 16 through 247 or resid 255 through 827 or resid 849 throu \ gh 1147)) } 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.090 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4879 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 : 0.002 0.037 29144 Z= 0.103 Angle : 0.437 5.490 39693 Z= 0.253 Chirality : 0.041 0.143 4482 Planarity : 0.002 0.033 5138 Dihedral : 8.283 84.683 10430 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.25 % Favored : 97.56 % Rotamer: Outliers : 0.03 % Allowed : 0.00 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: 1.00 (0.14), residues: 3605 helix: 2.57 (0.21), residues: 650 sheet: 0.89 (0.17), residues: 892 loop : -0.02 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.009 0.001 TYR E 144 PHE 0.009 0.001 PHE D 490 TRP 0.004 0.001 TRP A 47 HIS 0.003 0.000 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00185 (29101) covalent geometry : angle 0.43622 (39606) SS BOND : bond 0.00095 ( 42) SS BOND : angle 0.63842 ( 84) hydrogen bonds : bond 0.22244 ( 1081) hydrogen bonds : angle 8.74292 ( 3072) link_NAG-ASN : bond 0.00005 ( 1) link_NAG-ASN : angle 2.85228 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 844 time to evaluate : 0.858 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 105 ILE cc_start: 0.8784 (mt) cc_final: 0.8494 (tt) REVERT: E 117 LEU cc_start: 0.8542 (tp) cc_final: 0.8305 (tt) REVERT: E 287 ASP cc_start: 0.8227 (t0) cc_final: 0.8006 (m-30) REVERT: E 306 PHE cc_start: 0.7081 (p90) cc_final: 0.6878 (m-80) REVERT: E 493 GLN cc_start: 0.8638 (mt0) cc_final: 0.8401 (mp10) REVERT: E 532 ASN cc_start: 0.7972 (m-40) cc_final: 0.7746 (p0) REVERT: E 720 ILE cc_start: 0.8395 (mm) cc_final: 0.7962 (pt) REVERT: E 731 MET cc_start: -0.1873 (ttp) cc_final: -0.2086 (tmm) REVERT: E 736 VAL cc_start: 0.3567 (t) cc_final: 0.3110 (p) REVERT: E 804 GLN cc_start: 0.7379 (mm-40) cc_final: 0.6853 (mm-40) REVERT: E 858 LEU cc_start: -0.0318 (mp) cc_final: -0.0897 (mt) REVERT: E 870 ILE cc_start: 0.7843 (mt) cc_final: 0.7609 (mp) REVERT: E 898 PHE cc_start: 0.7645 (t80) cc_final: 0.7403 (t80) REVERT: E 963 VAL cc_start: 0.5475 (t) cc_final: 0.5084 (t) REVERT: E 1017 GLU cc_start: 0.6669 (mm-30) cc_final: 0.2823 (pt0) REVERT: E 1018 ILE cc_start: 0.3942 (mm) cc_final: 0.3723 (mm) REVERT: E 1028 LYS cc_start: 0.6656 (mttt) cc_final: 0.6289 (mtpt) REVERT: E 1029 MET cc_start: 0.8002 (tpp) cc_final: 0.7785 (mmp) REVERT: E 1038 LYS cc_start: 0.8756 (mttm) cc_final: 0.8470 (mmtm) REVERT: E 1062 PHE cc_start: 0.7423 (m-10) cc_final: 0.7144 (m-10) REVERT: A 177 GLN cc_start: 0.0825 (tp40) cc_final: 0.0515 (tt0) REVERT: A 195 PRO cc_start: 0.4340 (Cg_endo) cc_final: 0.4047 (Cg_exo) REVERT: B 47 GLN cc_start: 0.5868 (mt0) cc_final: 0.5658 (tp40) REVERT: B 58 ASN cc_start: 0.3626 (m-40) cc_final: 0.3125 (m-40) REVERT: B 108 LYS cc_start: 0.5902 (tttt) cc_final: 0.5520 (tptp) REVERT: B 111 ILE cc_start: 0.4729 (mm) cc_final: 0.4052 (mt) REVERT: B 162 ASN cc_start: 0.6184 (m-40) cc_final: 0.5882 (t0) REVERT: C 169 GLU cc_start: 0.8548 (tt0) cc_final: 0.8345 (tm-30) REVERT: C 193 VAL cc_start: 0.7605 (t) cc_final: 0.7389 (t) REVERT: C 238 PHE cc_start: 0.7762 (p90) cc_final: 0.7537 (p90) REVERT: C 302 THR cc_start: 0.6181 (m) cc_final: 0.5969 (p) REVERT: C 303 LEU cc_start: 0.6058 (mt) cc_final: 0.5833 (mm) REVERT: C 382 VAL cc_start: 0.5283 (m) cc_final: 0.4938 (p) REVERT: C 546 LEU cc_start: 0.6468 (tp) cc_final: 0.6206 (tt) REVERT: C 559 PHE cc_start: -0.1872 (m-10) cc_final: -0.2260 (m-10) REVERT: C 597 VAL cc_start: 0.5596 (t) cc_final: 0.5332 (t) REVERT: C 599 THR cc_start: 0.2900 (t) cc_final: 0.1748 (t) REVERT: C 654 GLU cc_start: 0.7913 (tt0) cc_final: 0.7698 (mm-30) REVERT: C 664 ILE cc_start: 0.2927 (mt) cc_final: 0.2677 (mt) REVERT: C 752 LEU cc_start: 0.8243 (mt) cc_final: 0.7966 (tp) REVERT: C 772 VAL cc_start: 0.8841 (t) cc_final: 0.8364 (t) REVERT: C 773 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8793 (mm-30) REVERT: C 859 THR cc_start: 0.6646 (m) cc_final: 0.6246 (p) REVERT: C 867 ASP cc_start: 0.7626 (m-30) cc_final: 0.7396 (p0) REVERT: C 947 LYS cc_start: 0.9039 (mttt) cc_final: 0.8468 (mtpt) REVERT: C 957 GLN cc_start: 0.9344 (mt0) cc_final: 0.9079 (pt0) REVERT: C 979 ASP cc_start: 0.8620 (t70) cc_final: 0.8414 (t0) REVERT: C 984 LEU cc_start: 0.5759 (mp) cc_final: 0.5536 (mt) REVERT: C 997 ILE cc_start: 0.7275 (mt) cc_final: 0.6427 (mm) REVERT: C 1002 GLN cc_start: 0.8758 (mp10) cc_final: 0.8529 (pt0) REVERT: C 1013 ILE cc_start: 0.9025 (mt) cc_final: 0.8606 (mt) REVERT: D 225 PRO cc_start: 0.4503 (Cg_exo) cc_final: 0.4234 (Cg_endo) REVERT: D 302 THR cc_start: 0.6535 (m) cc_final: 0.5814 (p) REVERT: D 460 ASN cc_start: 0.8842 (m-40) cc_final: 0.8514 (t0) REVERT: D 532 ASN cc_start: 0.7564 (m-40) cc_final: 0.7254 (t0) REVERT: D 572 THR cc_start: 0.6788 (p) cc_final: 0.6445 (m) REVERT: D 658 ASN cc_start: 0.8240 (m-40) cc_final: 0.7991 (t0) REVERT: D 710 ASN cc_start: 0.7253 (m110) cc_final: 0.7013 (t0) REVERT: D 723 THR cc_start: 0.8642 (m) cc_final: 0.8420 (p) REVERT: D 736 VAL cc_start: 0.6594 (t) cc_final: 0.6382 (t) REVERT: D 737 ASP cc_start: 0.8401 (t0) cc_final: 0.7994 (p0) REVERT: D 753 LEU cc_start: 0.2329 (tp) cc_final: 0.1708 (tp) REVERT: D 756 TYR cc_start: 0.2430 (m-80) cc_final: 0.1794 (m-10) REVERT: D 759 PHE cc_start: 0.5781 (m-10) cc_final: 0.5014 (m-80) REVERT: D 777 ASN cc_start: 0.8838 (m-40) cc_final: 0.8455 (m-40) REVERT: D 787 GLN cc_start: 0.7973 (mt0) cc_final: 0.7530 (mt0) REVERT: D 874 THR cc_start: 0.9261 (m) cc_final: 0.9057 (p) REVERT: D 947 LYS cc_start: 0.9164 (mttt) cc_final: 0.8939 (mmtm) REVERT: D 980 ILE cc_start: 0.4793 (mt) cc_final: 0.2633 (mt) REVERT: D 984 LEU cc_start: 0.4822 (mt) cc_final: 0.3662 (mp) REVERT: D 1010 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7980 (tp-100) REVERT: D 1036 GLN cc_start: 0.6641 (tt0) cc_final: 0.5942 (tt0) REVERT: D 1061 VAL cc_start: 0.8639 (t) cc_final: 0.8418 (t) REVERT: D 1065 VAL cc_start: 0.9217 (t) cc_final: 0.8456 (t) REVERT: D 1073 LYS cc_start: 0.8569 (tttt) cc_final: 0.7898 (tptt) outliers start: 1 outliers final: 0 residues processed: 845 average time/residue: 0.1829 time to fit residues: 237.7948 Evaluate side-chains 421 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 6.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS E 134 GLN E 394 ASN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 955 ASN ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1083 HIS A 65 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 194 HIS C 188 ASN C 207 HIS C 394 ASN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 606 ASN C 784 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 928 ASN C1010 GLN C1088 HIS C1101 HIS C1142 GLN D 52 GLN D 66 HIS D 69 HIS D 245 HIS D 762 GLN D 856 ASN ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.069527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.059663 restraints weight = 283169.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.060858 restraints weight = 160299.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.061648 restraints weight = 102395.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.062216 restraints weight = 70871.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.062676 restraints weight = 53653.746| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 29144 Z= 0.311 Angle : 0.838 12.396 39693 Z= 0.439 Chirality : 0.050 0.260 4482 Planarity : 0.006 0.089 5138 Dihedral : 5.007 58.941 3925 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.11 % Favored : 95.70 % Rotamer: Outliers : 0.16 % Allowed : 2.83 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: 0.05 (0.13), residues: 3605 helix: 1.04 (0.19), residues: 712 sheet: 0.39 (0.16), residues: 913 loop : -0.48 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 995 TYR 0.038 0.003 TYR E 145 PHE 0.026 0.003 PHE C 338 TRP 0.043 0.003 TRP A 50 HIS 0.009 0.003 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00656 (29101) covalent geometry : angle 0.83470 (39606) SS BOND : bond 0.00680 ( 42) SS BOND : angle 1.40993 ( 84) hydrogen bonds : bond 0.05444 ( 1081) hydrogen bonds : angle 6.98573 ( 3072) link_NAG-ASN : bond 0.00066 ( 1) link_NAG-ASN : angle 6.34079 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 437 time to evaluate : 1.107 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 ASP cc_start: 0.8518 (t0) cc_final: 0.8103 (m-30) REVERT: E 304 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8142 (tppt) REVERT: E 493 GLN cc_start: 0.8659 (mt0) cc_final: 0.8382 (mp10) REVERT: E 532 ASN cc_start: 0.8363 (m-40) cc_final: 0.8039 (p0) REVERT: E 740 MET cc_start: 0.8074 (tpp) cc_final: 0.7836 (tpp) REVERT: E 818 ILE cc_start: 0.8965 (mt) cc_final: 0.8584 (mt) REVERT: E 864 LEU cc_start: 0.9056 (tp) cc_final: 0.8793 (tp) REVERT: E 1028 LYS cc_start: 0.9134 (mttt) cc_final: 0.8921 (mtpt) REVERT: E 1029 MET cc_start: 0.8721 (tpp) cc_final: 0.8337 (mmm) REVERT: E 1033 VAL cc_start: 0.8644 (t) cc_final: 0.7559 (t) REVERT: E 1047 TYR cc_start: 0.8313 (m-80) cc_final: 0.8026 (m-10) REVERT: E 1062 PHE cc_start: 0.8654 (m-10) cc_final: 0.8308 (m-80) REVERT: A 63 LYS cc_start: 0.7273 (mttt) cc_final: 0.6993 (tttt) REVERT: A 214 LYS cc_start: 0.3174 (mmmt) cc_final: 0.2622 (tptt) REVERT: B 58 ASN cc_start: 0.3955 (m-40) cc_final: 0.3669 (m-40) REVERT: B 162 ASN cc_start: 0.6240 (m-40) cc_final: 0.5993 (t0) REVERT: C 52 GLN cc_start: 0.9151 (tt0) cc_final: 0.8035 (pm20) REVERT: C 58 PHE cc_start: 0.7498 (m-10) cc_final: 0.7250 (m-10) REVERT: C 269 TYR cc_start: 0.7244 (m-10) cc_final: 0.6931 (m-80) REVERT: C 314 GLN cc_start: 0.8015 (tt0) cc_final: 0.7736 (tm-30) REVERT: C 697 MET cc_start: 0.8112 (ttm) cc_final: 0.7825 (mtp) REVERT: C 731 MET cc_start: 0.7904 (ttm) cc_final: 0.7670 (ttm) REVERT: C 732 THR cc_start: 0.8692 (m) cc_final: 0.8492 (p) REVERT: C 752 LEU cc_start: 0.8861 (mt) cc_final: 0.8092 (tp) REVERT: C 772 VAL cc_start: 0.9229 (t) cc_final: 0.9013 (p) REVERT: C 904 TYR cc_start: 0.8791 (t80) cc_final: 0.8344 (t80) REVERT: C 1001 LEU cc_start: 0.9116 (tp) cc_final: 0.8856 (tt) REVERT: C 1006 THR cc_start: 0.9345 (p) cc_final: 0.8787 (p) REVERT: C 1010 GLN cc_start: 0.9095 (mt0) cc_final: 0.8723 (mm-40) REVERT: C 1013 ILE cc_start: 0.9656 (mt) cc_final: 0.9212 (mt) REVERT: C 1017 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8805 (pm20) REVERT: C 1018 ILE cc_start: 0.9297 (mt) cc_final: 0.9040 (tt) REVERT: C 1031 GLU cc_start: 0.8601 (mt-10) cc_final: 0.7998 (mt-10) REVERT: C 1052 PHE cc_start: 0.8602 (m-10) cc_final: 0.8137 (m-10) REVERT: D 302 THR cc_start: 0.8711 (m) cc_final: 0.8440 (p) REVERT: D 455 LEU cc_start: 0.7920 (tp) cc_final: 0.7646 (tp) REVERT: D 464 PHE cc_start: 0.7994 (m-80) cc_final: 0.7644 (m-10) REVERT: D 532 ASN cc_start: 0.7557 (m-40) cc_final: 0.7223 (t0) REVERT: D 697 MET cc_start: 0.7946 (ttm) cc_final: 0.7460 (mtp) REVERT: D 723 THR cc_start: 0.8935 (m) cc_final: 0.8674 (p) REVERT: D 875 SER cc_start: 0.8935 (t) cc_final: 0.8701 (p) REVERT: D 904 TYR cc_start: 0.8399 (t80) cc_final: 0.7782 (t80) REVERT: D 1001 LEU cc_start: 0.9502 (mt) cc_final: 0.9266 (mt) REVERT: D 1019 ARG cc_start: 0.8185 (tmt170) cc_final: 0.7935 (ttp80) REVERT: D 1029 MET cc_start: 0.8508 (tmm) cc_final: 0.8217 (tmm) outliers start: 5 outliers final: 0 residues processed: 442 average time/residue: 0.1617 time to fit residues: 113.5740 Evaluate side-chains 248 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 312 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 GLN ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 47 GLN B 95 GLN C 394 ASN C 481 ASN C1002 GLN D 450 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN D 925 ASN D 955 ASN D1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.063535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.051875 restraints weight = 232514.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.053135 restraints weight = 143202.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.053997 restraints weight = 97806.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.054548 restraints weight = 72468.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.054967 restraints weight = 57700.347| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29144 Z= 0.140 Angle : 0.573 11.329 39693 Z= 0.300 Chirality : 0.044 0.192 4482 Planarity : 0.004 0.059 5138 Dihedral : 4.491 57.287 3925 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.97 % Favored : 96.84 % Rotamer: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: 0.10 (0.13), residues: 3605 helix: 1.16 (0.19), residues: 722 sheet: 0.41 (0.16), residues: 922 loop : -0.48 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 403 TYR 0.021 0.002 TYR A 32 PHE 0.042 0.002 PHE E 342 TRP 0.025 0.002 TRP A 50 HIS 0.006 0.001 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00308 (29101) covalent geometry : angle 0.56795 (39606) SS BOND : bond 0.00417 ( 42) SS BOND : angle 1.39009 ( 84) hydrogen bonds : bond 0.04133 ( 1081) hydrogen bonds : angle 6.31267 ( 3072) link_NAG-ASN : bond 0.00054 ( 1) link_NAG-ASN : angle 4.95637 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 0.823 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 490 PHE cc_start: 0.2536 (t80) cc_final: 0.2281 (t80) REVERT: E 493 GLN cc_start: 0.8686 (mt0) cc_final: 0.8403 (mm-40) REVERT: E 532 ASN cc_start: 0.8429 (m-40) cc_final: 0.8015 (p0) REVERT: E 740 MET cc_start: 0.7906 (tpp) cc_final: 0.7675 (tpp) REVERT: E 864 LEU cc_start: 0.8953 (tp) cc_final: 0.8502 (tp) REVERT: E 945 LEU cc_start: 0.9013 (pp) cc_final: 0.8666 (pp) REVERT: E 949 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7890 (mm-40) REVERT: E 1023 ASN cc_start: 0.8835 (m110) cc_final: 0.8503 (m110) REVERT: E 1033 VAL cc_start: 0.8536 (t) cc_final: 0.7904 (t) REVERT: A 63 LYS cc_start: 0.6992 (mttt) cc_final: 0.6684 (tttt) REVERT: A 214 LYS cc_start: 0.3031 (mmmt) cc_final: 0.2377 (tptp) REVERT: B 58 ASN cc_start: 0.4127 (m-40) cc_final: 0.3795 (m-40) REVERT: B 162 ASN cc_start: 0.6712 (m-40) cc_final: 0.6341 (t0) REVERT: C 269 TYR cc_start: 0.7489 (m-10) cc_final: 0.7134 (m-10) REVERT: C 394 ASN cc_start: 0.6480 (OUTLIER) cc_final: 0.4787 (t0) REVERT: C 559 PHE cc_start: 0.6766 (m-80) cc_final: 0.6462 (m-80) REVERT: C 697 MET cc_start: 0.8229 (ttm) cc_final: 0.7623 (mtp) REVERT: C 752 LEU cc_start: 0.8829 (mt) cc_final: 0.7830 (tp) REVERT: C 904 TYR cc_start: 0.8777 (t80) cc_final: 0.8254 (t80) REVERT: C 1018 ILE cc_start: 0.9306 (mt) cc_final: 0.8862 (tt) REVERT: C 1031 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8094 (mt-10) REVERT: C 1055 SER cc_start: 0.8236 (t) cc_final: 0.8036 (t) REVERT: D 302 THR cc_start: 0.8731 (m) cc_final: 0.8515 (p) REVERT: D 464 PHE cc_start: 0.7949 (m-80) cc_final: 0.7682 (m-10) REVERT: D 492 LEU cc_start: 0.8250 (mp) cc_final: 0.8014 (tp) REVERT: D 532 ASN cc_start: 0.7595 (m-40) cc_final: 0.7213 (t0) REVERT: D 742 ILE cc_start: 0.8039 (mt) cc_final: 0.7644 (tp) REVERT: D 909 ILE cc_start: 0.8938 (pt) cc_final: 0.8724 (mt) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.1763 time to fit residues: 106.8610 Evaluate side-chains 245 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 323 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 354 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 319 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 895 GLN E 949 GLN ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 613 GLN C 777 ASN C1002 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.062959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.051185 restraints weight = 234360.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.052431 restraints weight = 143016.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.053304 restraints weight = 97565.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.053879 restraints weight = 72084.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.054316 restraints weight = 56981.366| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29144 Z= 0.145 Angle : 0.565 12.000 39693 Z= 0.293 Chirality : 0.043 0.184 4482 Planarity : 0.004 0.051 5138 Dihedral : 4.489 56.583 3925 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: 0.01 (0.13), residues: 3605 helix: 1.11 (0.20), residues: 717 sheet: 0.39 (0.16), residues: 912 loop : -0.57 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 815 TYR 0.020 0.002 TYR D 365 PHE 0.023 0.002 PHE D 855 TRP 0.045 0.002 TRP A 50 HIS 0.007 0.001 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00316 (29101) covalent geometry : angle 0.56099 (39606) SS BOND : bond 0.00403 ( 42) SS BOND : angle 1.21474 ( 84) hydrogen bonds : bond 0.03891 ( 1081) hydrogen bonds : angle 6.12642 ( 3072) link_NAG-ASN : bond 0.00147 ( 1) link_NAG-ASN : angle 4.79882 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 1.129 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 304 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8334 (tptm) REVERT: E 493 GLN cc_start: 0.8709 (mt0) cc_final: 0.8416 (mp-120) REVERT: E 532 ASN cc_start: 0.8451 (m-40) cc_final: 0.8037 (p0) REVERT: E 740 MET cc_start: 0.7974 (tpp) cc_final: 0.7715 (tpp) REVERT: E 864 LEU cc_start: 0.8847 (tp) cc_final: 0.8464 (tp) REVERT: E 950 ASP cc_start: 0.8672 (t0) cc_final: 0.7688 (t0) REVERT: E 954 GLN cc_start: 0.8686 (pt0) cc_final: 0.8396 (pt0) REVERT: E 1023 ASN cc_start: 0.8824 (m110) cc_final: 0.8496 (m110) REVERT: E 1029 MET cc_start: 0.8516 (mmp) cc_final: 0.7031 (mmp) REVERT: E 1030 SER cc_start: 0.9184 (m) cc_final: 0.8896 (p) REVERT: A 63 LYS cc_start: 0.6843 (mttt) cc_final: 0.6491 (tttt) REVERT: A 214 LYS cc_start: 0.3268 (mmmt) cc_final: 0.2655 (tptt) REVERT: B 58 ASN cc_start: 0.4182 (m-40) cc_final: 0.3855 (m-40) REVERT: B 162 ASN cc_start: 0.6795 (m-40) cc_final: 0.6369 (t0) REVERT: C 52 GLN cc_start: 0.9061 (tt0) cc_final: 0.8014 (pm20) REVERT: C 269 TYR cc_start: 0.7456 (m-10) cc_final: 0.7113 (m-10) REVERT: C 559 PHE cc_start: 0.6796 (m-80) cc_final: 0.6590 (m-80) REVERT: C 697 MET cc_start: 0.8124 (ttm) cc_final: 0.7735 (mtp) REVERT: C 721 SER cc_start: 0.9020 (m) cc_final: 0.8811 (p) REVERT: C 752 LEU cc_start: 0.8847 (mt) cc_final: 0.7821 (tp) REVERT: C 904 TYR cc_start: 0.8696 (t80) cc_final: 0.8187 (t80) REVERT: C 945 LEU cc_start: 0.7582 (tt) cc_final: 0.7122 (mp) REVERT: C 957 GLN cc_start: 0.8487 (tp-100) cc_final: 0.8121 (tp-100) REVERT: C 1006 THR cc_start: 0.8937 (p) cc_final: 0.8687 (p) REVERT: C 1010 GLN cc_start: 0.8941 (mt0) cc_final: 0.8647 (mm-40) REVERT: D 302 THR cc_start: 0.8721 (m) cc_final: 0.8517 (p) REVERT: D 464 PHE cc_start: 0.7870 (m-80) cc_final: 0.7639 (m-10) REVERT: D 492 LEU cc_start: 0.8277 (mp) cc_final: 0.8025 (tp) REVERT: D 532 ASN cc_start: 0.7745 (m-40) cc_final: 0.7264 (t0) REVERT: D 731 MET cc_start: 0.8984 (ttp) cc_final: 0.8725 (ttm) REVERT: D 742 ILE cc_start: 0.8081 (mt) cc_final: 0.7678 (tp) REVERT: D 774 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8671 (mm-40) REVERT: D 864 LEU cc_start: 0.8811 (tp) cc_final: 0.8186 (tp) REVERT: D 869 MET cc_start: 0.8485 (ptp) cc_final: 0.8251 (ptp) REVERT: D 1089 PHE cc_start: 0.8326 (m-80) cc_final: 0.7862 (m-80) outliers start: 1 outliers final: 1 residues processed: 346 average time/residue: 0.1490 time to fit residues: 84.3878 Evaluate side-chains 234 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 100 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 254 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 ASN E 23 GLN E 134 GLN E 394 ASN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 98 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 762 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN ** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.059170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.048326 restraints weight = 252748.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.049528 restraints weight = 153446.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.050352 restraints weight = 103511.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.050952 restraints weight = 75652.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.051423 restraints weight = 58097.935| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 29144 Z= 0.389 Angle : 0.895 13.878 39693 Z= 0.472 Chirality : 0.051 0.222 4482 Planarity : 0.007 0.062 5138 Dihedral : 6.094 58.657 3925 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.46 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: -0.93 (0.13), residues: 3605 helix: 0.23 (0.19), residues: 731 sheet: -0.19 (0.16), residues: 881 loop : -1.13 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 403 TYR 0.043 0.004 TYR D 313 PHE 0.039 0.004 PHE C 592 TRP 0.047 0.004 TRP A 50 HIS 0.011 0.003 HIS D1064 Details of bonding type rmsd covalent geometry : bond 0.00823 (29101) covalent geometry : angle 0.88991 (39606) SS BOND : bond 0.00740 ( 42) SS BOND : angle 1.89128 ( 84) hydrogen bonds : bond 0.05436 ( 1081) hydrogen bonds : angle 7.12649 ( 3072) link_NAG-ASN : bond 0.00039 ( 1) link_NAG-ASN : angle 7.15801 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.103 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 304 LYS cc_start: 0.9040 (mmtm) cc_final: 0.8461 (tptm) REVERT: E 532 ASN cc_start: 0.8782 (m-40) cc_final: 0.8377 (p0) REVERT: E 562 PHE cc_start: 0.7382 (m-80) cc_final: 0.7179 (m-80) REVERT: E 704 SER cc_start: 0.8903 (t) cc_final: 0.8613 (p) REVERT: E 740 MET cc_start: 0.8020 (tpp) cc_final: 0.7727 (tpp) REVERT: E 1030 SER cc_start: 0.9158 (m) cc_final: 0.8812 (p) REVERT: C 697 MET cc_start: 0.8010 (ttm) cc_final: 0.7773 (mtp) REVERT: C 721 SER cc_start: 0.9150 (m) cc_final: 0.8681 (t) REVERT: C 869 MET cc_start: 0.8876 (tpp) cc_final: 0.8502 (tpp) REVERT: C 904 TYR cc_start: 0.8635 (t80) cc_final: 0.8265 (t80) REVERT: C 921 LYS cc_start: 0.9106 (mttt) cc_final: 0.8864 (pttp) REVERT: C 945 LEU cc_start: 0.8229 (tt) cc_final: 0.7648 (mm) REVERT: C 957 GLN cc_start: 0.8789 (tp-100) cc_final: 0.8279 (tp-100) REVERT: C 990 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7909 (mt-10) REVERT: C 1018 ILE cc_start: 0.9160 (mt) cc_final: 0.8853 (tt) REVERT: C 1029 MET cc_start: 0.8479 (tpp) cc_final: 0.8227 (mmp) REVERT: C 1051 SER cc_start: 0.8012 (t) cc_final: 0.7753 (p) REVERT: D 532 ASN cc_start: 0.7899 (m-40) cc_final: 0.7434 (t0) REVERT: D 571 ASP cc_start: 0.8839 (m-30) cc_final: 0.8579 (t0) REVERT: D 774 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8950 (mm-40) REVERT: D 864 LEU cc_start: 0.9218 (tp) cc_final: 0.8749 (tp) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1602 time to fit residues: 76.0633 Evaluate side-chains 181 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 254 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 317 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 275 optimal weight: 4.9990 chunk 59 optimal weight: 0.0270 chunk 110 optimal weight: 9.9990 chunk 140 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 ASN E 23 GLN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN B 194 HIS C 394 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C1002 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN D 762 GLN D 895 GLN D 935 GLN D1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.067900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.058396 restraints weight = 281444.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.059592 restraints weight = 155808.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.060362 restraints weight = 97728.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.060924 restraints weight = 67544.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.061308 restraints weight = 50627.834| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.6283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29144 Z= 0.142 Angle : 0.603 14.274 39693 Z= 0.312 Chirality : 0.045 0.214 4482 Planarity : 0.005 0.051 5138 Dihedral : 5.171 50.384 3925 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.91 % Favored : 95.89 % Rotamer: Outliers : 0.03 % Allowed : 1.41 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: -0.60 (0.13), residues: 3605 helix: 0.72 (0.19), residues: 728 sheet: -0.10 (0.17), residues: 873 loop : -0.95 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1019 TYR 0.033 0.002 TYR C 38 PHE 0.025 0.002 PHE D 275 TRP 0.046 0.002 TRP A 50 HIS 0.006 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00314 (29101) covalent geometry : angle 0.59796 (39606) SS BOND : bond 0.00440 ( 42) SS BOND : angle 1.46560 ( 84) hydrogen bonds : bond 0.03960 ( 1081) hydrogen bonds : angle 6.36173 ( 3072) link_NAG-ASN : bond 0.00031 ( 1) link_NAG-ASN : angle 5.63810 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 0.783 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 360 ASN cc_start: 0.6576 (t0) cc_final: 0.6367 (t0) REVERT: E 448 ASN cc_start: 0.6846 (t0) cc_final: 0.5462 (m110) REVERT: E 449 TYR cc_start: 0.5132 (m-10) cc_final: 0.4903 (m-80) REVERT: E 453 TYR cc_start: 0.8360 (p90) cc_final: 0.8073 (p90) REVERT: E 532 ASN cc_start: 0.8435 (m-40) cc_final: 0.8131 (p0) REVERT: E 562 PHE cc_start: 0.7261 (m-80) cc_final: 0.7035 (m-80) REVERT: E 740 MET cc_start: 0.7699 (tpp) cc_final: 0.7424 (tpp) REVERT: E 752 LEU cc_start: 0.8873 (mm) cc_final: 0.8287 (mt) REVERT: E 926 GLN cc_start: 0.8843 (mt0) cc_final: 0.8494 (mt0) REVERT: E 950 ASP cc_start: 0.8517 (t0) cc_final: 0.7201 (t0) REVERT: E 954 GLN cc_start: 0.8607 (pt0) cc_final: 0.8276 (pt0) REVERT: E 973 ILE cc_start: 0.7838 (mt) cc_final: 0.7568 (mt) REVERT: E 1023 ASN cc_start: 0.8803 (m110) cc_final: 0.8565 (m110) REVERT: E 1027 THR cc_start: 0.9055 (m) cc_final: 0.8731 (p) REVERT: E 1030 SER cc_start: 0.9110 (m) cc_final: 0.8774 (p) REVERT: E 1050 MET cc_start: 0.8628 (pmm) cc_final: 0.8023 (pmm) REVERT: C 52 GLN cc_start: 0.9140 (tt0) cc_final: 0.8205 (pm20) REVERT: C 721 SER cc_start: 0.9084 (m) cc_final: 0.8766 (t) REVERT: C 752 LEU cc_start: 0.9059 (mt) cc_final: 0.8776 (tp) REVERT: C 777 ASN cc_start: 0.7519 (m-40) cc_final: 0.6993 (m-40) REVERT: C 869 MET cc_start: 0.8518 (tpp) cc_final: 0.8224 (tpp) REVERT: C 921 LYS cc_start: 0.9055 (mttt) cc_final: 0.8840 (pttp) REVERT: C 945 LEU cc_start: 0.7941 (tt) cc_final: 0.7355 (mm) REVERT: C 957 GLN cc_start: 0.8488 (tp-100) cc_final: 0.8044 (tp-100) REVERT: C 1006 THR cc_start: 0.9201 (p) cc_final: 0.8976 (p) REVERT: C 1018 ILE cc_start: 0.9190 (mt) cc_final: 0.8799 (tt) REVERT: D 215 ASP cc_start: 0.7830 (m-30) cc_final: 0.7609 (m-30) REVERT: D 229 LEU cc_start: 0.9104 (mt) cc_final: 0.8903 (mt) REVERT: D 302 THR cc_start: 0.8758 (m) cc_final: 0.8548 (p) REVERT: D 532 ASN cc_start: 0.7590 (m-40) cc_final: 0.7184 (t0) REVERT: D 742 ILE cc_start: 0.8107 (mt) cc_final: 0.7764 (tp) REVERT: D 774 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8743 (mm-40) REVERT: D 864 LEU cc_start: 0.9073 (tp) cc_final: 0.8452 (tp) outliers start: 1 outliers final: 0 residues processed: 312 average time/residue: 0.1528 time to fit residues: 78.6916 Evaluate side-chains 213 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 230 optimal weight: 0.9990 chunk 350 optimal weight: 0.6980 chunk 262 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 327 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.061763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.050635 restraints weight = 250149.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.051873 restraints weight = 151722.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.052662 restraints weight = 102459.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.053338 restraints weight = 75208.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.053744 restraints weight = 57669.178| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29144 Z= 0.123 Angle : 0.570 12.104 39693 Z= 0.296 Chirality : 0.044 0.230 4482 Planarity : 0.004 0.068 5138 Dihedral : 4.833 51.094 3925 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.94 % Favored : 95.87 % Rotamer: Outliers : 0.03 % Allowed : 0.97 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: -0.49 (0.14), residues: 3605 helix: 0.81 (0.19), residues: 729 sheet: -0.02 (0.17), residues: 871 loop : -0.87 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.021 0.002 TYR D 917 PHE 0.024 0.002 PHE D 275 TRP 0.043 0.002 TRP A 50 HIS 0.006 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00274 (29101) covalent geometry : angle 0.56557 (39606) SS BOND : bond 0.00389 ( 42) SS BOND : angle 1.32752 ( 84) hydrogen bonds : bond 0.03763 ( 1081) hydrogen bonds : angle 6.07251 ( 3072) link_NAG-ASN : bond 0.00215 ( 1) link_NAG-ASN : angle 4.65188 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 1.054 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: symmetry clash REVERT: E 175 PHE cc_start: 0.2516 (p90) cc_final: 0.1552 (t80) REVERT: E 448 ASN cc_start: 0.7022 (t0) cc_final: 0.5561 (m110) REVERT: E 449 TYR cc_start: 0.5245 (m-10) cc_final: 0.5030 (m-80) REVERT: E 493 GLN cc_start: 0.8516 (mt0) cc_final: 0.8296 (mp10) REVERT: E 532 ASN cc_start: 0.8604 (m-40) cc_final: 0.8194 (p0) REVERT: E 740 MET cc_start: 0.7828 (tpp) cc_final: 0.7472 (tpp) REVERT: E 752 LEU cc_start: 0.8875 (mm) cc_final: 0.8531 (mt) REVERT: E 864 LEU cc_start: 0.8971 (tp) cc_final: 0.8755 (tt) REVERT: E 926 GLN cc_start: 0.8670 (mt0) cc_final: 0.8441 (mt0) REVERT: E 973 ILE cc_start: 0.7822 (mt) cc_final: 0.7587 (mt) REVERT: E 1023 ASN cc_start: 0.8901 (m110) cc_final: 0.8626 (m110) REVERT: E 1029 MET cc_start: 0.8791 (mmp) cc_final: 0.7800 (mmm) REVERT: E 1030 SER cc_start: 0.9150 (m) cc_final: 0.8818 (p) REVERT: C 52 GLN cc_start: 0.9118 (tt0) cc_final: 0.8210 (pm20) REVERT: C 559 PHE cc_start: 0.6280 (m-80) cc_final: 0.5921 (m-80) REVERT: C 721 SER cc_start: 0.9172 (m) cc_final: 0.8841 (t) REVERT: C 752 LEU cc_start: 0.9190 (mt) cc_final: 0.8901 (tp) REVERT: C 777 ASN cc_start: 0.7826 (m110) cc_final: 0.7374 (m110) REVERT: C 869 MET cc_start: 0.8714 (tpp) cc_final: 0.8489 (tpp) REVERT: C 902 MET cc_start: 0.8715 (mmm) cc_final: 0.8405 (mmm) REVERT: C 921 LYS cc_start: 0.9146 (mttt) cc_final: 0.8834 (pttp) REVERT: C 945 LEU cc_start: 0.8094 (tt) cc_final: 0.7460 (mm) REVERT: C 957 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8221 (tp-100) REVERT: C 1018 ILE cc_start: 0.9119 (mt) cc_final: 0.8848 (tt) REVERT: C 1019 ARG cc_start: 0.9297 (ptt-90) cc_final: 0.8801 (ptt90) REVERT: C 1031 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8468 (mm-30) REVERT: D 304 LYS cc_start: 0.9184 (mptt) cc_final: 0.8811 (mmtt) REVERT: D 532 ASN cc_start: 0.7831 (m-40) cc_final: 0.7275 (t0) REVERT: D 742 ILE cc_start: 0.8145 (mt) cc_final: 0.7753 (tp) REVERT: D 774 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8848 (mm-40) REVERT: D 1010 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8860 (tp40) REVERT: D 1050 MET cc_start: 0.8623 (pmm) cc_final: 0.8278 (pmm) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.1607 time to fit residues: 81.0655 Evaluate side-chains 215 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 64 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 341 optimal weight: 10.0000 chunk 327 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 313 optimal weight: 0.9990 chunk 271 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN ** D 935 GLN ** 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 = 0.3687 r_free = 0.3687 target = 0.060871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.049809 restraints weight = 250747.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.051035 restraints weight = 153220.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.051924 restraints weight = 103628.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.052559 restraints weight = 74388.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.052974 restraints weight = 57467.559| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29144 Z= 0.166 Angle : 0.608 12.594 39693 Z= 0.316 Chirality : 0.045 0.237 4482 Planarity : 0.004 0.063 5138 Dihedral : 4.942 56.349 3925 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.63 % Favored : 95.17 % Rotamer: Outliers : 0.03 % Allowed : 0.82 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: -0.59 (0.14), residues: 3605 helix: 0.67 (0.19), residues: 731 sheet: -0.14 (0.17), residues: 891 loop : -0.89 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1019 TYR 0.035 0.002 TYR C 741 PHE 0.027 0.002 PHE E1062 TRP 0.041 0.002 TRP A 50 HIS 0.026 0.002 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00367 (29101) covalent geometry : angle 0.60308 (39606) SS BOND : bond 0.00437 ( 42) SS BOND : angle 1.47017 ( 84) hydrogen bonds : bond 0.03949 ( 1081) hydrogen bonds : angle 6.11241 ( 3072) link_NAG-ASN : bond 0.00383 ( 1) link_NAG-ASN : angle 4.90185 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 1.041 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 175 PHE cc_start: 0.2532 (p90) cc_final: 0.1495 (t80) REVERT: E 360 ASN cc_start: 0.6557 (t0) cc_final: 0.6339 (t0) REVERT: E 448 ASN cc_start: 0.7132 (t0) cc_final: 0.5708 (m110) REVERT: E 449 TYR cc_start: 0.5459 (m-10) cc_final: 0.5221 (m-80) REVERT: E 493 GLN cc_start: 0.8483 (mt0) cc_final: 0.8272 (mp10) REVERT: E 532 ASN cc_start: 0.8628 (m-40) cc_final: 0.8243 (p0) REVERT: E 562 PHE cc_start: 0.7306 (m-80) cc_final: 0.7062 (m-80) REVERT: E 740 MET cc_start: 0.7705 (tpp) cc_final: 0.7368 (tpp) REVERT: E 864 LEU cc_start: 0.9036 (tp) cc_final: 0.8681 (tt) REVERT: E 926 GLN cc_start: 0.8673 (mt0) cc_final: 0.8396 (mt0) REVERT: E 973 ILE cc_start: 0.7777 (mt) cc_final: 0.7514 (mt) REVERT: E 1023 ASN cc_start: 0.8859 (m110) cc_final: 0.8594 (m110) REVERT: E 1030 SER cc_start: 0.9110 (m) cc_final: 0.8762 (p) REVERT: E 1050 MET cc_start: 0.8921 (pmm) cc_final: 0.8674 (pmm) REVERT: C 559 PHE cc_start: 0.6438 (m-80) cc_final: 0.6097 (m-80) REVERT: C 697 MET cc_start: 0.7627 (mtp) cc_final: 0.7260 (mtp) REVERT: C 721 SER cc_start: 0.9185 (m) cc_final: 0.8844 (t) REVERT: C 752 LEU cc_start: 0.9113 (mt) cc_final: 0.8816 (tp) REVERT: C 777 ASN cc_start: 0.7672 (m110) cc_final: 0.7340 (m110) REVERT: C 902 MET cc_start: 0.8727 (mmm) cc_final: 0.8298 (mmm) REVERT: C 921 LYS cc_start: 0.9135 (mttt) cc_final: 0.8869 (pttp) REVERT: C 957 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8173 (tp-100) REVERT: C 1018 ILE cc_start: 0.9175 (mt) cc_final: 0.8910 (tt) REVERT: C 1029 MET cc_start: 0.8299 (tpp) cc_final: 0.8027 (mmp) REVERT: C 1031 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8429 (mm-30) REVERT: D 229 LEU cc_start: 0.9158 (mt) cc_final: 0.8953 (mt) REVERT: D 532 ASN cc_start: 0.7754 (m-40) cc_final: 0.7255 (t0) REVERT: D 571 ASP cc_start: 0.8853 (m-30) cc_final: 0.8315 (t0) REVERT: D 742 ILE cc_start: 0.8165 (mt) cc_final: 0.7799 (tp) REVERT: D 774 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8810 (mm-40) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.1551 time to fit residues: 71.9544 Evaluate side-chains 198 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 249 optimal weight: 0.7980 chunk 238 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 23 GLN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.059520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.048609 restraints weight = 252399.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.049782 restraints weight = 153495.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.050640 restraints weight = 103363.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.051162 restraints weight = 74646.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.051640 restraints weight = 58065.649| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.7192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29144 Z= 0.235 Angle : 0.702 14.295 39693 Z= 0.369 Chirality : 0.047 0.337 4482 Planarity : 0.005 0.067 5138 Dihedral : 5.511 59.741 3925 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.02 % Favored : 93.79 % Rotamer: Outliers : 0.03 % Allowed : 0.66 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: -0.88 (0.13), residues: 3605 helix: 0.53 (0.19), residues: 730 sheet: -0.33 (0.17), residues: 867 loop : -1.12 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 403 TYR 0.052 0.003 TYR C 741 PHE 0.028 0.002 PHE C 133 TRP 0.040 0.003 TRP A 50 HIS 0.023 0.002 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00504 (29101) covalent geometry : angle 0.69650 (39606) SS BOND : bond 0.00583 ( 42) SS BOND : angle 1.75942 ( 84) hydrogen bonds : bond 0.04470 ( 1081) hydrogen bonds : angle 6.48195 ( 3072) link_NAG-ASN : bond 0.00018 ( 1) link_NAG-ASN : angle 6.10189 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.989 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 177 MET cc_start: 0.3554 (tmm) cc_final: -0.0685 (mpp) REVERT: E 214 ARG cc_start: 0.7112 (tpp80) cc_final: 0.6837 (tpp-160) REVERT: E 360 ASN cc_start: 0.6668 (t0) cc_final: 0.6429 (t0) REVERT: E 448 ASN cc_start: 0.7306 (t0) cc_final: 0.6120 (m110) REVERT: E 532 ASN cc_start: 0.8779 (m-40) cc_final: 0.8373 (p0) REVERT: E 562 PHE cc_start: 0.7418 (m-80) cc_final: 0.7125 (m-80) REVERT: E 740 MET cc_start: 0.7773 (tpp) cc_final: 0.7515 (tpp) REVERT: E 864 LEU cc_start: 0.8979 (tp) cc_final: 0.8719 (tt) REVERT: E 926 GLN cc_start: 0.8746 (mt0) cc_final: 0.8447 (mt0) REVERT: E 973 ILE cc_start: 0.7856 (mt) cc_final: 0.7559 (mt) REVERT: E 1023 ASN cc_start: 0.8864 (m110) cc_final: 0.8591 (m110) REVERT: E 1030 SER cc_start: 0.9142 (m) cc_final: 0.8751 (p) REVERT: E 1050 MET cc_start: 0.8595 (pmm) cc_final: 0.8376 (pmm) REVERT: B 168 TRP cc_start: 0.4847 (t60) cc_final: 0.4569 (t60) REVERT: C 697 MET cc_start: 0.7779 (mtp) cc_final: 0.7429 (mtp) REVERT: C 721 SER cc_start: 0.9126 (m) cc_final: 0.8671 (t) REVERT: C 752 LEU cc_start: 0.9134 (mt) cc_final: 0.8758 (tp) REVERT: C 902 MET cc_start: 0.8760 (mmm) cc_final: 0.8380 (mmm) REVERT: C 904 TYR cc_start: 0.8670 (t80) cc_final: 0.8404 (t80) REVERT: C 945 LEU cc_start: 0.7767 (tp) cc_final: 0.7337 (mp) REVERT: C 957 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8105 (tp-100) REVERT: C 1029 MET cc_start: 0.8378 (tpp) cc_final: 0.8142 (mmp) REVERT: C 1031 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8336 (mm-30) REVERT: C 1050 MET cc_start: 0.8030 (ptm) cc_final: 0.7780 (ptm) REVERT: D 532 ASN cc_start: 0.7776 (m-40) cc_final: 0.7354 (t0) REVERT: D 571 ASP cc_start: 0.8838 (m-30) cc_final: 0.8373 (t0) REVERT: D 731 MET cc_start: 0.8935 (ttp) cc_final: 0.8399 (ttm) REVERT: D 742 ILE cc_start: 0.8116 (mt) cc_final: 0.7870 (tp) REVERT: D 774 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8913 (mm-40) outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.1451 time to fit residues: 63.5608 Evaluate side-chains 186 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 174 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 221 optimal weight: 0.7980 chunk 293 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 ASN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN C 99 ASN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 953 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 = 0.3653 r_free = 0.3653 target = 0.059940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.049314 restraints weight = 252078.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.050523 restraints weight = 153761.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.051284 restraints weight = 103367.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.051967 restraints weight = 74669.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.052485 restraints weight = 57460.741| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29144 Z= 0.194 Angle : 0.650 15.608 39693 Z= 0.340 Chirality : 0.046 0.244 4482 Planarity : 0.005 0.071 5138 Dihedral : 5.408 58.350 3925 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.56 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: -0.94 (0.13), residues: 3605 helix: 0.47 (0.19), residues: 736 sheet: -0.36 (0.17), residues: 848 loop : -1.15 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1014 TYR 0.042 0.002 TYR C 741 PHE 0.020 0.002 PHE D 275 TRP 0.040 0.002 TRP E 152 HIS 0.018 0.002 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00422 (29101) covalent geometry : angle 0.64415 (39606) SS BOND : bond 0.00470 ( 42) SS BOND : angle 1.65487 ( 84) hydrogen bonds : bond 0.04225 ( 1081) hydrogen bonds : angle 6.39051 ( 3072) link_NAG-ASN : bond 0.00047 ( 1) link_NAG-ASN : angle 5.66553 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7210 Ramachandran restraints generated. 3605 Oldfield, 0 Emsley, 3605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 1.057 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 177 MET cc_start: 0.2932 (tmm) cc_final: -0.0990 (mpp) REVERT: E 448 ASN cc_start: 0.7057 (t0) cc_final: 0.5996 (m110) REVERT: E 532 ASN cc_start: 0.8838 (m-40) cc_final: 0.8396 (p0) REVERT: E 740 MET cc_start: 0.7860 (tpp) cc_final: 0.7577 (tpp) REVERT: E 864 LEU cc_start: 0.8977 (tp) cc_final: 0.8664 (tt) REVERT: E 926 GLN cc_start: 0.8776 (mt0) cc_final: 0.8464 (mt0) REVERT: E 950 ASP cc_start: 0.8771 (t0) cc_final: 0.8253 (p0) REVERT: E 973 ILE cc_start: 0.7898 (mt) cc_final: 0.7604 (mt) REVERT: E 1023 ASN cc_start: 0.8835 (m110) cc_final: 0.8537 (m110) REVERT: E 1030 SER cc_start: 0.9206 (m) cc_final: 0.8860 (p) REVERT: E 1031 GLU cc_start: 0.7850 (tt0) cc_final: 0.7090 (mt-10) REVERT: E 1050 MET cc_start: 0.8690 (pmm) cc_final: 0.8015 (pmm) REVERT: B 168 TRP cc_start: 0.4908 (t60) cc_final: 0.4547 (t60) REVERT: C 52 GLN cc_start: 0.9129 (tt0) cc_final: 0.8276 (pm20) REVERT: C 697 MET cc_start: 0.7725 (mtp) cc_final: 0.7319 (mtp) REVERT: C 721 SER cc_start: 0.9140 (m) cc_final: 0.8649 (t) REVERT: C 752 LEU cc_start: 0.9183 (mt) cc_final: 0.8821 (tp) REVERT: C 902 MET cc_start: 0.8790 (mmm) cc_final: 0.8537 (mmm) REVERT: C 904 TYR cc_start: 0.8700 (t80) cc_final: 0.8338 (t80) REVERT: C 945 LEU cc_start: 0.7889 (tp) cc_final: 0.7555 (mp) REVERT: C 954 GLN cc_start: 0.9272 (tp-100) cc_final: 0.8969 (tp40) REVERT: C 957 GLN cc_start: 0.8718 (tp-100) cc_final: 0.8250 (tp-100) REVERT: C 1019 ARG cc_start: 0.9228 (ptt-90) cc_final: 0.8729 (ptt90) REVERT: C 1031 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8264 (mm-30) REVERT: D 532 ASN cc_start: 0.7795 (m-40) cc_final: 0.7346 (t0) REVERT: D 571 ASP cc_start: 0.8859 (m-30) cc_final: 0.8358 (t0) REVERT: D 731 MET cc_start: 0.8785 (ttp) cc_final: 0.8061 (ttm) REVERT: D 742 ILE cc_start: 0.8226 (mt) cc_final: 0.7929 (tp) REVERT: D 774 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8781 (mm-40) REVERT: D 900 MET cc_start: 0.8076 (mpp) cc_final: 0.7464 (mtt) REVERT: D 1014 ARG cc_start: 0.8530 (mtp-110) cc_final: 0.8155 (ttm170) outliers start: 1 outliers final: 0 residues processed: 256 average time/residue: 0.1609 time to fit residues: 68.8950 Evaluate side-chains 192 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 320 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 79 optimal weight: 0.0570 chunk 29 optimal weight: 0.3980 chunk 248 optimal weight: 4.9990 chunk 333 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 957 GLN ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN C 394 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C1002 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 953 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 = 0.3682 r_free = 0.3682 target = 0.060562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.049569 restraints weight = 246495.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.050768 restraints weight = 152090.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.051644 restraints weight = 103167.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.052263 restraints weight = 74505.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.052655 restraints weight = 57690.765| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.7231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29144 Z= 0.128 Angle : 0.600 13.798 39693 Z= 0.310 Chirality : 0.045 0.194 4482 Planarity : 0.004 0.067 5138 Dihedral : 5.081 57.688 3925 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.69 % Favored : 95.12 % Rotamer: Outliers : 0.06 % Allowed : 0.22 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % 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 aren not related in a simple way. whole: -0.77 (0.14), residues: 3605 helix: 0.63 (0.19), residues: 738 sheet: -0.25 (0.17), residues: 858 loop : -1.06 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 214 TYR 0.037 0.002 TYR C 741 PHE 0.027 0.002 PHE E 65 TRP 0.034 0.002 TRP E 152 HIS 0.016 0.001 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00289 (29101) covalent geometry : angle 0.59461 (39606) SS BOND : bond 0.00365 ( 42) SS BOND : angle 1.52666 ( 84) hydrogen bonds : bond 0.03836 ( 1081) hydrogen bonds : angle 6.06728 ( 3072) link_NAG-ASN : bond 0.00132 ( 1) link_NAG-ASN : angle 5.04869 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4455.38 seconds wall clock time: 78 minutes 20.37 seconds (4700.37 seconds total)