Starting phenix.real_space_refine on Mon May 26 19:20:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k9b_36983/05_2025/8k9b_36983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9b_36983/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k9b_36983/05_2025/8k9b_36983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9b_36983/05_2025/8k9b_36983.map" model { file = "/net/cci-nas-00/data/ceres_data/8k9b_36983/05_2025/8k9b_36983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9b_36983/05_2025/8k9b_36983.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.32, per 1000 atoms: 0.57 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: 7.05 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 4.97 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: 15.69 Time building geometry restraints manager: 8.17 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.260 Process input model: 69.880 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.260 ------------------------------------------------------------------------------- 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 : 3.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP A 47 HIS 0.003 0.000 HIS B 31 PHE 0.009 0.001 PHE D 490 TYR 0.009 0.001 TYR E 144 ARG 0.004 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00005 ( 1) link_NAG-ASN : angle 2.85228 ( 3) hydrogen bonds : bond 0.22244 ( 1081) hydrogen bonds : angle 8.74292 ( 3072) SS BOND : bond 0.00095 ( 42) SS BOND : angle 0.63842 ( 84) covalent geometry : bond 0.00185 (29101) covalent geometry : angle 0.43622 (39606) *********************** 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 : 3.115 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: E 105 ILE cc_start: 0.8784 (mt) cc_final: 0.8496 (tt) REVERT: E 117 LEU cc_start: 0.8542 (tp) cc_final: 0.8291 (tt) REVERT: E 196 ASN cc_start: 0.6015 (t0) cc_final: 0.5792 (m-40) REVERT: E 287 ASP cc_start: 0.8227 (t0) cc_final: 0.8008 (m-30) REVERT: E 493 GLN cc_start: 0.8638 (mt0) cc_final: 0.8400 (mp10) REVERT: E 532 ASN cc_start: 0.7972 (m-40) cc_final: 0.7746 (p0) REVERT: E 666 ILE cc_start: 0.4044 (mt) cc_final: 0.3805 (mt) REVERT: E 720 ILE cc_start: 0.8395 (mm) cc_final: 0.7962 (pt) REVERT: E 736 VAL cc_start: 0.3567 (t) cc_final: 0.3099 (p) REVERT: E 804 GLN cc_start: 0.7379 (mm-40) cc_final: 0.6850 (mm-40) REVERT: E 858 LEU cc_start: -0.0318 (mp) cc_final: -0.0872 (mt) REVERT: E 898 PHE cc_start: 0.7645 (t80) cc_final: 0.7407 (t80) REVERT: E 963 VAL cc_start: 0.5475 (t) cc_final: 0.5079 (t) REVERT: E 1017 GLU cc_start: 0.6669 (mm-30) cc_final: 0.2748 (pt0) REVERT: E 1028 LYS cc_start: 0.6656 (mttt) cc_final: 0.6288 (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: 0.8476 (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: 0.0529 (tt0) REVERT: A 195 PRO cc_start: 0.4340 (Cg_endo) cc_final: 0.4049 (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: 0.3128 (m-40) REVERT: B 108 LYS cc_start: 0.5902 (tttt) cc_final: 0.5525 (tptp) REVERT: B 111 ILE cc_start: 0.4729 (mm) cc_final: 0.4054 (mt) REVERT: B 162 ASN cc_start: 0.6184 (m-40) cc_final: 0.5886 (t0) REVERT: C 169 GLU cc_start: 0.8548 (tt0) cc_final: 0.8340 (tm-30) REVERT: C 193 VAL cc_start: 0.7605 (t) cc_final: 0.7387 (t) REVERT: C 238 PHE cc_start: 0.7762 (p90) cc_final: 0.7530 (p90) REVERT: C 302 THR cc_start: 0.6181 (m) cc_final: 0.5973 (p) REVERT: C 303 LEU cc_start: 0.6058 (mt) cc_final: 0.5843 (mm) REVERT: C 382 VAL cc_start: 0.5283 (m) cc_final: 0.4961 (p) REVERT: C 546 LEU cc_start: 0.6468 (tp) cc_final: 0.6218 (tt) REVERT: C 559 PHE cc_start: -0.1872 (m-10) cc_final: -0.2258 (m-10) REVERT: C 597 VAL cc_start: 0.5596 (t) cc_final: 0.5328 (t) REVERT: C 599 THR cc_start: 0.2900 (t) cc_final: 0.1734 (t) REVERT: C 654 GLU cc_start: 0.7913 (tt0) cc_final: 0.7697 (mm-30) REVERT: C 664 ILE cc_start: 0.2927 (mt) cc_final: 0.2669 (mt) REVERT: C 752 LEU cc_start: 0.8243 (mt) cc_final: 0.7953 (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: 0.6248 (p) REVERT: C 867 ASP cc_start: 0.7626 (m-30) cc_final: 0.7383 (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: 0.9067 (pt0) REVERT: C 984 LEU cc_start: 0.5759 (mp) cc_final: 0.5540 (mt) REVERT: C 997 ILE cc_start: 0.7275 (mt) cc_final: 0.6344 (mm) REVERT: C 1002 GLN cc_start: 0.8758 (mp10) cc_final: 0.8541 (pt0) REVERT: C 1013 ILE cc_start: 0.9025 (mt) cc_final: 0.8598 (mt) REVERT: D 225 PRO cc_start: 0.4503 (Cg_exo) cc_final: 0.4240 (Cg_endo) REVERT: D 302 THR cc_start: 0.6535 (m) cc_final: 0.5813 (p) 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: 0.6451 (m) REVERT: D 710 ASN cc_start: 0.7253 (m110) cc_final: 0.7028 (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: 0.6353 (t) REVERT: D 737 ASP cc_start: 0.8401 (t0) cc_final: 0.7985 (p0) REVERT: D 753 LEU cc_start: 0.2329 (tp) cc_final: 0.1753 (tp) REVERT: D 756 TYR cc_start: 0.2430 (m-80) cc_final: 0.1608 (m-10) REVERT: D 759 PHE cc_start: 0.5781 (m-10) cc_final: 0.4689 (m-80) REVERT: D 777 ASN cc_start: 0.8838 (m-40) cc_final: 0.8451 (m-40) REVERT: D 787 GLN cc_start: 0.7973 (mt0) cc_final: 0.7531 (mt0) REVERT: D 874 THR cc_start: 0.9261 (m) cc_final: 0.9058 (p) REVERT: D 947 LYS cc_start: 0.9164 (mttt) cc_final: 0.8944 (mmtm) REVERT: D 980 ILE cc_start: 0.4793 (mt) cc_final: 0.2753 (mt) REVERT: D 984 LEU cc_start: 0.4822 (mt) cc_final: 0.3653 (mp) REVERT: D 1010 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7979 (tp-100) REVERT: D 1036 GLN cc_start: 0.6641 (tt0) cc_final: 0.6149 (tt0) REVERT: D 1061 VAL cc_start: 0.8639 (t) cc_final: 0.8268 (t) REVERT: D 1065 VAL cc_start: 0.9217 (t) cc_final: 0.8466 (t) REVERT: D 1073 LYS cc_start: 0.8569 (tttt) cc_final: 0.8049 (tptt) outliers start: 1 outliers final: 0 residues processed: 845 average time/residue: 0.4197 time to fit residues: 542.1874 Evaluate side-chains 417 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 282 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 327 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 HIS E 394 ASN E 710 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 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1083 HIS ** 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 856 ASN ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN D1023 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.069540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.059716 restraints weight = 282620.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.060904 restraints weight = 160494.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.061612 restraints weight = 102263.699| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 29144 Z= 0.321 Angle : 0.848 12.725 39693 Z= 0.445 Chirality : 0.051 0.269 4482 Planarity : 0.006 0.086 5138 Dihedral : 5.063 58.854 3925 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.13 % Favored : 95.67 % Rotamer: Outliers : 0.19 % Allowed : 3.11 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 3605 helix: 0.91 (0.19), residues: 711 sheet: 0.44 (0.16), residues: 902 loop : -0.48 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 50 HIS 0.008 0.003 HIS A 170 PHE 0.027 0.003 PHE C1052 TYR 0.038 0.003 TYR E 145 ARG 0.018 0.002 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 1) link_NAG-ASN : angle 6.40370 ( 3) hydrogen bonds : bond 0.05435 ( 1081) hydrogen bonds : angle 6.99412 ( 3072) SS BOND : bond 0.00646 ( 42) SS BOND : angle 1.42176 ( 84) covalent geometry : bond 0.00674 (29101) covalent geometry : angle 0.84502 (39606) *********************** 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 441 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 435 time to evaluate : 3.367 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 304 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8372 (tptm) REVERT: E 493 GLN cc_start: 0.8688 (mt0) cc_final: 0.8355 (mp10) REVERT: E 532 ASN cc_start: 0.8382 (m-40) cc_final: 0.8056 (p0) REVERT: E 818 ILE cc_start: 0.8947 (mt) cc_final: 0.8545 (mt) REVERT: E 864 LEU cc_start: 0.9022 (tp) cc_final: 0.8768 (tp) REVERT: E 1029 MET cc_start: 0.8722 (tpp) cc_final: 0.8341 (mmm) REVERT: E 1033 VAL cc_start: 0.8669 (t) cc_final: 0.7550 (t) REVERT: E 1047 TYR cc_start: 0.8324 (m-80) cc_final: 0.8055 (m-10) REVERT: E 1062 PHE cc_start: 0.8646 (m-10) cc_final: 0.8246 (m-80) REVERT: A 63 LYS cc_start: 0.7281 (mttt) cc_final: 0.7000 (tttt) REVERT: A 214 LYS cc_start: 0.3132 (mmmt) cc_final: 0.2546 (tptt) REVERT: B 58 ASN cc_start: 0.3969 (m-40) cc_final: 0.3684 (m-40) REVERT: B 162 ASN cc_start: 0.6315 (m-40) cc_final: 0.6047 (t0) REVERT: C 52 GLN cc_start: 0.9174 (tt0) cc_final: 0.8087 (pm20) REVERT: C 58 PHE cc_start: 0.7507 (m-10) cc_final: 0.7265 (m-10) REVERT: C 269 TYR cc_start: 0.7367 (m-10) cc_final: 0.7028 (m-80) REVERT: C 314 GLN cc_start: 0.7987 (tt0) cc_final: 0.7749 (tm-30) REVERT: C 772 VAL cc_start: 0.9254 (t) cc_final: 0.9038 (p) REVERT: C 854 LYS cc_start: 0.3048 (pttt) cc_final: 0.2802 (pttt) REVERT: C 904 TYR cc_start: 0.8742 (t80) cc_final: 0.8415 (t80) REVERT: C 1001 LEU cc_start: 0.9160 (tp) cc_final: 0.8899 (tt) REVERT: C 1013 ILE cc_start: 0.9637 (mt) cc_final: 0.9244 (mt) REVERT: C 1017 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8812 (pm20) REVERT: C 1018 ILE cc_start: 0.9373 (mt) cc_final: 0.9121 (tt) REVERT: C 1031 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8018 (mt-10) REVERT: C 1052 PHE cc_start: 0.8653 (m-10) cc_final: 0.8232 (m-10) REVERT: D 302 THR cc_start: 0.8719 (m) cc_final: 0.8442 (p) REVERT: D 455 LEU cc_start: 0.7919 (tp) cc_final: 0.7644 (tp) REVERT: D 464 PHE cc_start: 0.8160 (m-80) cc_final: 0.7755 (m-10) REVERT: D 532 ASN cc_start: 0.7586 (m-40) cc_final: 0.7248 (t0) REVERT: D 697 MET cc_start: 0.7915 (ttm) cc_final: 0.7683 (mtp) REVERT: D 723 THR cc_start: 0.8925 (m) cc_final: 0.8671 (p) REVERT: D 731 MET cc_start: 0.8857 (ttp) cc_final: 0.8232 (ttm) REVERT: D 774 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8950 (mm110) REVERT: D 875 SER cc_start: 0.8956 (t) cc_final: 0.8705 (p) REVERT: D 904 TYR cc_start: 0.8433 (t80) cc_final: 0.7823 (t80) REVERT: D 1019 ARG cc_start: 0.8093 (tmt170) cc_final: 0.7843 (ttp80) REVERT: D 1029 MET cc_start: 0.8609 (tmm) cc_final: 0.8281 (tmm) outliers start: 6 outliers final: 1 residues processed: 441 average time/residue: 0.4208 time to fit residues: 290.3703 Evaluate side-chains 249 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 354 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 203 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 303 optimal weight: 0.0570 chunk 32 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 208 optimal weight: 0.1980 chunk 202 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- 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 949 GLN E 957 GLN 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 C1010 GLN C1101 HIS D 450 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.071433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.061753 restraints weight = 279362.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.063000 restraints weight = 156763.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.063788 restraints weight = 98430.531| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4458 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= 0.130 Angle : 0.569 11.467 39693 Z= 0.296 Chirality : 0.044 0.166 4482 Planarity : 0.004 0.074 5138 Dihedral : 4.441 56.800 3925 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.13), residues: 3605 helix: 1.19 (0.20), residues: 711 sheet: 0.45 (0.16), residues: 931 loop : -0.50 (0.13), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 50 HIS 0.006 0.001 HIS C1101 PHE 0.042 0.002 PHE E 342 TYR 0.025 0.002 TYR E 873 ARG 0.008 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 1) link_NAG-ASN : angle 4.67470 ( 3) hydrogen bonds : bond 0.04093 ( 1081) hydrogen bonds : angle 6.24538 ( 3072) SS BOND : bond 0.00372 ( 42) SS BOND : angle 1.45960 ( 84) covalent geometry : bond 0.00284 (29101) covalent geometry : angle 0.56445 (39606) *********************** 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 393 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 2.999 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 193 VAL cc_start: 0.8912 (t) cc_final: 0.8708 (t) REVERT: E 194 PHE cc_start: 0.6624 (m-80) cc_final: 0.6298 (m-80) REVERT: E 340 GLU cc_start: 0.8330 (pt0) cc_final: 0.7817 (pp20) REVERT: E 493 GLN cc_start: 0.8759 (mt0) cc_final: 0.8469 (mm-40) REVERT: E 532 ASN cc_start: 0.8383 (m-40) cc_final: 0.8008 (p0) REVERT: E 740 MET cc_start: 0.7896 (tpp) cc_final: 0.7658 (tpp) REVERT: E 864 LEU cc_start: 0.8989 (tp) cc_final: 0.8526 (tp) REVERT: E 945 LEU cc_start: 0.8974 (pp) cc_final: 0.8626 (pp) REVERT: E 949 GLN cc_start: 0.8229 (mm110) cc_final: 0.7911 (mm-40) REVERT: E 1023 ASN cc_start: 0.8813 (m110) cc_final: 0.8471 (m110) REVERT: E 1033 VAL cc_start: 0.8603 (t) cc_final: 0.7946 (t) REVERT: A 63 LYS cc_start: 0.7133 (mttt) cc_final: 0.6857 (tttt) REVERT: A 214 LYS cc_start: 0.3180 (mmmt) cc_final: 0.2505 (tptp) REVERT: B 58 ASN cc_start: 0.4100 (m-40) cc_final: 0.3750 (m-40) REVERT: B 162 ASN cc_start: 0.6361 (m-40) cc_final: 0.6097 (t0) REVERT: B 168 TRP cc_start: 0.3613 (t60) cc_final: 0.3382 (t60) REVERT: C 269 TYR cc_start: 0.7317 (m-10) cc_final: 0.6989 (m-10) REVERT: C 697 MET cc_start: 0.7867 (mtp) cc_final: 0.7655 (mtp) REVERT: C 752 LEU cc_start: 0.8855 (mt) cc_final: 0.7875 (tp) REVERT: C 904 TYR cc_start: 0.8773 (t80) cc_final: 0.8334 (t80) REVERT: C 950 ASP cc_start: 0.8467 (m-30) cc_final: 0.8146 (t0) REVERT: C 957 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8254 (tp-100) REVERT: C 962 LEU cc_start: 0.9032 (tp) cc_final: 0.8759 (tp) REVERT: C 1018 ILE cc_start: 0.9247 (mt) cc_final: 0.8896 (tt) REVERT: C 1052 PHE cc_start: 0.8679 (m-10) cc_final: 0.8390 (m-10) REVERT: C 1055 SER cc_start: 0.8129 (t) cc_final: 0.7920 (t) REVERT: D 302 THR cc_start: 0.8676 (m) cc_final: 0.8453 (p) REVERT: D 464 PHE cc_start: 0.7946 (m-80) cc_final: 0.7626 (m-10) REVERT: D 532 ASN cc_start: 0.7520 (m-40) cc_final: 0.7158 (t0) REVERT: D 723 THR cc_start: 0.8857 (m) cc_final: 0.8607 (p) REVERT: D 774 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8923 (mm-40) REVERT: D 909 ILE cc_start: 0.8940 (pt) cc_final: 0.8685 (mt) REVERT: D 1004 LEU cc_start: 0.9045 (mt) cc_final: 0.8826 (mt) REVERT: D 1031 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8357 (mp0) REVERT: D 1089 PHE cc_start: 0.8138 (m-80) cc_final: 0.7761 (m-80) outliers start: 1 outliers final: 0 residues processed: 393 average time/residue: 0.3874 time to fit residues: 243.5783 Evaluate side-chains 255 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 321 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 350 optimal weight: 6.9990 chunk 302 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 304 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 955 ASN ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN B 6 GLN B 47 GLN C 394 ASN C 542 ASN C 613 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.062332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.050867 restraints weight = 242149.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.052106 restraints weight = 148675.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.052947 restraints weight = 101369.269| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29144 Z= 0.187 Angle : 0.603 12.199 39693 Z= 0.314 Chirality : 0.044 0.195 4482 Planarity : 0.004 0.048 5138 Dihedral : 4.646 58.153 3925 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.08 % Favored : 95.73 % Rotamer: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 3605 helix: 1.09 (0.20), residues: 719 sheet: 0.35 (0.16), residues: 906 loop : -0.61 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 50 HIS 0.006 0.001 HIS C1101 PHE 0.023 0.002 PHE D 855 TYR 0.021 0.002 TYR E 873 ARG 0.011 0.001 ARG C 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 1) link_NAG-ASN : angle 5.16936 ( 3) hydrogen bonds : bond 0.04054 ( 1081) hydrogen bonds : angle 6.22307 ( 3072) SS BOND : bond 0.00572 ( 42) SS BOND : angle 1.27819 ( 84) covalent geometry : bond 0.00401 (29101) covalent geometry : angle 0.59903 (39606) *********************** 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 333 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 331 time to evaluate : 3.163 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: E 493 GLN cc_start: 0.8680 (mt0) cc_final: 0.8478 (mp10) REVERT: E 532 ASN cc_start: 0.8549 (m-40) cc_final: 0.8105 (p0) REVERT: E 740 MET cc_start: 0.7904 (tpp) cc_final: 0.7685 (tpp) REVERT: E 864 LEU cc_start: 0.8930 (tp) cc_final: 0.8640 (tp) REVERT: E 973 ILE cc_start: 0.7819 (mt) cc_final: 0.7577 (mt) REVERT: E 1023 ASN cc_start: 0.8827 (m110) cc_final: 0.8497 (m110) REVERT: E 1030 SER cc_start: 0.9232 (m) cc_final: 0.8914 (p) REVERT: A 214 LYS cc_start: 0.3239 (mmmt) cc_final: 0.2629 (tptt) REVERT: B 58 ASN cc_start: 0.4268 (m-40) cc_final: 0.3959 (m-40) REVERT: B 162 ASN cc_start: 0.6697 (m-40) cc_final: 0.6299 (t0) REVERT: C 52 GLN cc_start: 0.9168 (tt0) cc_final: 0.8032 (pm20) REVERT: C 269 TYR cc_start: 0.7490 (m-10) cc_final: 0.7173 (m-10) REVERT: C 721 SER cc_start: 0.9068 (m) cc_final: 0.8773 (t) REVERT: C 752 LEU cc_start: 0.8929 (mt) cc_final: 0.7985 (tp) REVERT: C 773 GLU cc_start: 0.8048 (tp30) cc_final: 0.7738 (tp30) REVERT: C 777 ASN cc_start: 0.8506 (m-40) cc_final: 0.7163 (m-40) REVERT: C 902 MET cc_start: 0.8734 (mmm) cc_final: 0.8488 (mmm) REVERT: C 904 TYR cc_start: 0.8665 (t80) cc_final: 0.8304 (t80) REVERT: C 945 LEU cc_start: 0.7750 (tt) cc_final: 0.7230 (mp) REVERT: C 957 GLN cc_start: 0.8486 (tp-100) cc_final: 0.8259 (tp-100) REVERT: C 962 LEU cc_start: 0.9159 (tp) cc_final: 0.8892 (tp) REVERT: C 1018 ILE cc_start: 0.9289 (mt) cc_final: 0.8896 (tt) REVERT: C 1019 ARG cc_start: 0.9286 (ptt-90) cc_final: 0.8595 (ptt90) REVERT: C 1031 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8115 (mt-10) REVERT: D 302 THR cc_start: 0.8723 (m) cc_final: 0.8501 (p) REVERT: D 464 PHE cc_start: 0.7970 (m-80) cc_final: 0.7686 (m-10) REVERT: D 532 ASN cc_start: 0.7688 (m-40) cc_final: 0.7220 (t0) REVERT: D 742 ILE cc_start: 0.8053 (mt) cc_final: 0.7723 (tp) REVERT: D 774 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8709 (mm-40) REVERT: D 1089 PHE cc_start: 0.8357 (m-80) cc_final: 0.7880 (m-80) outliers start: 2 outliers final: 1 residues processed: 332 average time/residue: 0.3822 time to fit residues: 205.8097 Evaluate side-chains 232 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 339 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 288 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 104 optimal weight: 0.0050 chunk 187 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 895 GLN ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN C 762 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN D1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.062272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.050958 restraints weight = 244881.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.052225 restraints weight = 149780.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.053101 restraints weight = 101439.983| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29144 Z= 0.161 Angle : 0.576 13.012 39693 Z= 0.299 Chirality : 0.044 0.186 4482 Planarity : 0.004 0.050 5138 Dihedral : 4.665 57.247 3925 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.91 % Favored : 95.89 % Rotamer: Outliers : 0.03 % Allowed : 1.44 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 3605 helix: 1.02 (0.20), residues: 724 sheet: 0.24 (0.16), residues: 909 loop : -0.70 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 50 HIS 0.008 0.001 HIS C1101 PHE 0.020 0.002 PHE D 800 TYR 0.031 0.002 TYR E1047 ARG 0.008 0.001 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 1) link_NAG-ASN : angle 5.14843 ( 3) hydrogen bonds : bond 0.03807 ( 1081) hydrogen bonds : angle 6.10988 ( 3072) SS BOND : bond 0.00374 ( 42) SS BOND : angle 1.38215 ( 84) covalent geometry : bond 0.00349 (29101) covalent geometry : angle 0.57099 (39606) *********************** 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 327 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 3.122 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: E 287 ASP cc_start: 0.8750 (m-30) cc_final: 0.8527 (m-30) REVERT: E 493 GLN cc_start: 0.8648 (mt0) cc_final: 0.8399 (mp10) REVERT: E 532 ASN cc_start: 0.8596 (m-40) cc_final: 0.8175 (p0) REVERT: E 740 MET cc_start: 0.7920 (tpp) cc_final: 0.7581 (tpp) REVERT: E 752 LEU cc_start: 0.8750 (mm) cc_final: 0.8255 (mt) REVERT: E 754 LEU cc_start: 0.8914 (mm) cc_final: 0.8544 (tt) REVERT: E 864 LEU cc_start: 0.8940 (tp) cc_final: 0.8658 (tp) REVERT: E 973 ILE cc_start: 0.7809 (mt) cc_final: 0.7535 (mt) REVERT: E 1023 ASN cc_start: 0.8864 (m110) cc_final: 0.8497 (m110) REVERT: E 1030 SER cc_start: 0.9212 (m) cc_final: 0.8922 (p) REVERT: E 1050 MET cc_start: 0.8591 (pmm) cc_final: 0.8203 (pmm) REVERT: E 1062 PHE cc_start: 0.8347 (m-10) cc_final: 0.8095 (m-80) REVERT: A 78 THR cc_start: 0.7129 (m) cc_final: 0.6917 (m) REVERT: B 58 ASN cc_start: 0.4499 (m-40) cc_final: 0.4237 (m-40) REVERT: B 162 ASN cc_start: 0.6774 (m-40) cc_final: 0.6383 (t0) REVERT: C 52 GLN cc_start: 0.9155 (tt0) cc_final: 0.8068 (pm20) REVERT: C 721 SER cc_start: 0.9122 (m) cc_final: 0.8790 (t) REVERT: C 731 MET cc_start: 0.7877 (ttm) cc_final: 0.7630 (ttm) REVERT: C 752 LEU cc_start: 0.8987 (mt) cc_final: 0.8025 (tp) REVERT: C 773 GLU cc_start: 0.8203 (tp30) cc_final: 0.7717 (tp30) REVERT: C 777 ASN cc_start: 0.8424 (m-40) cc_final: 0.6930 (m-40) REVERT: C 902 MET cc_start: 0.8749 (mmm) cc_final: 0.8524 (mmm) REVERT: C 904 TYR cc_start: 0.8619 (t80) cc_final: 0.8338 (t80) REVERT: C 957 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8268 (tp-100) REVERT: C 962 LEU cc_start: 0.9181 (tp) cc_final: 0.8942 (tp) REVERT: C 988 GLU cc_start: 0.8433 (mp0) cc_final: 0.8197 (mp0) REVERT: C 1018 ILE cc_start: 0.9224 (mt) cc_final: 0.8948 (tt) REVERT: C 1019 ARG cc_start: 0.9312 (ptt-90) cc_final: 0.8969 (ptt90) REVERT: C 1031 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8264 (mt-10) REVERT: D 302 THR cc_start: 0.8704 (m) cc_final: 0.8472 (p) REVERT: D 464 PHE cc_start: 0.7969 (m-80) cc_final: 0.7693 (m-10) REVERT: D 532 ASN cc_start: 0.7795 (m-40) cc_final: 0.7296 (t0) REVERT: D 742 ILE cc_start: 0.8135 (mt) cc_final: 0.7725 (tp) REVERT: D 774 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8717 (mm-40) REVERT: D 1089 PHE cc_start: 0.8256 (m-80) cc_final: 0.7921 (m-80) outliers start: 1 outliers final: 1 residues processed: 327 average time/residue: 0.3686 time to fit residues: 198.7879 Evaluate side-chains 225 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 281 optimal weight: 0.8980 chunk 278 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 227 optimal weight: 0.0060 chunk 180 optimal weight: 0.0770 chunk 132 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 18 GLN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 777 ASN C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.070066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.056467 restraints weight = 186730.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.057347 restraints weight = 134834.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.057904 restraints weight = 107118.980| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29144 Z= 0.161 Angle : 0.583 12.672 39693 Z= 0.304 Chirality : 0.044 0.256 4482 Planarity : 0.004 0.076 5138 Dihedral : 4.758 56.875 3925 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.33 % Favored : 95.51 % Rotamer: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 3605 helix: 0.96 (0.20), residues: 726 sheet: 0.18 (0.17), residues: 882 loop : -0.73 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 50 HIS 0.008 0.001 HIS C1101 PHE 0.026 0.002 PHE E1075 TYR 0.025 0.002 TYR C 266 ARG 0.008 0.001 ARG D 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 1) link_NAG-ASN : angle 5.09632 ( 3) hydrogen bonds : bond 0.03796 ( 1081) hydrogen bonds : angle 6.07944 ( 3072) SS BOND : bond 0.00517 ( 42) SS BOND : angle 1.42409 ( 84) covalent geometry : bond 0.00347 (29101) covalent geometry : angle 0.57834 (39606) *********************** 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 317 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 3.101 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: E 304 LYS cc_start: 0.8976 (mmtm) cc_final: 0.8319 (tptm) REVERT: E 493 GLN cc_start: 0.8617 (mt0) cc_final: 0.8410 (mp10) REVERT: E 532 ASN cc_start: 0.8847 (m-40) cc_final: 0.8347 (p0) REVERT: E 740 MET cc_start: 0.7892 (tpp) cc_final: 0.7575 (tpp) REVERT: E 864 LEU cc_start: 0.8933 (tp) cc_final: 0.8715 (tp) REVERT: E 1023 ASN cc_start: 0.8925 (m110) cc_final: 0.8572 (m110) REVERT: E 1029 MET cc_start: 0.8881 (mmp) cc_final: 0.7041 (mmp) REVERT: E 1030 SER cc_start: 0.9196 (m) cc_final: 0.8909 (p) REVERT: E 1050 MET cc_start: 0.8678 (pmm) cc_final: 0.8093 (pmm) REVERT: E 1062 PHE cc_start: 0.8091 (m-10) cc_final: 0.7665 (m-80) REVERT: A 177 GLN cc_start: 0.2392 (tp40) cc_final: 0.1501 (pt0) REVERT: B 162 ASN cc_start: 0.7008 (m-40) cc_final: 0.6534 (t0) REVERT: C 52 GLN cc_start: 0.9239 (tt0) cc_final: 0.8102 (pm20) REVERT: C 229 LEU cc_start: 0.8428 (mt) cc_final: 0.8200 (mt) REVERT: C 559 PHE cc_start: 0.6425 (m-80) cc_final: 0.6019 (m-80) REVERT: C 613 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: C 721 SER cc_start: 0.9165 (m) cc_final: 0.8834 (t) REVERT: C 731 MET cc_start: 0.7780 (ttm) cc_final: 0.7497 (ttm) REVERT: C 773 GLU cc_start: 0.8363 (tp30) cc_final: 0.7804 (tp30) REVERT: C 777 ASN cc_start: 0.8357 (m110) cc_final: 0.6809 (m110) REVERT: C 904 TYR cc_start: 0.8678 (t80) cc_final: 0.8378 (t80) REVERT: C 921 LYS cc_start: 0.9076 (mttt) cc_final: 0.8798 (pttp) REVERT: C 957 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8187 (tp-100) REVERT: C 1018 ILE cc_start: 0.9101 (mt) cc_final: 0.8849 (tt) REVERT: C 1019 ARG cc_start: 0.9389 (ptt-90) cc_final: 0.9127 (ptt90) REVERT: C 1029 MET cc_start: 0.8399 (tpp) cc_final: 0.8184 (mmp) REVERT: C 1031 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8373 (mt-10) REVERT: D 215 ASP cc_start: 0.8160 (m-30) cc_final: 0.7956 (m-30) REVERT: D 302 THR cc_start: 0.8487 (m) cc_final: 0.8234 (p) REVERT: D 304 LYS cc_start: 0.9211 (mptt) cc_final: 0.8972 (mmtt) REVERT: D 464 PHE cc_start: 0.8189 (m-80) cc_final: 0.7920 (m-10) REVERT: D 532 ASN cc_start: 0.7982 (m-40) cc_final: 0.7384 (t0) REVERT: D 697 MET cc_start: 0.7708 (mmp) cc_final: 0.7203 (mmp) REVERT: D 742 ILE cc_start: 0.8137 (mt) cc_final: 0.7721 (tp) REVERT: D 774 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8731 (mm-40) REVERT: D 1001 LEU cc_start: 0.9496 (mt) cc_final: 0.9165 (mt) REVERT: D 1089 PHE cc_start: 0.8472 (m-80) cc_final: 0.8172 (m-80) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.3576 time to fit residues: 187.5920 Evaluate side-chains 229 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 112 optimal weight: 3.9990 chunk 244 optimal weight: 0.1980 chunk 346 optimal weight: 3.9990 chunk 319 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 18 GLN B 47 GLN B 142 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.069135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.059769 restraints weight = 281275.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.061195 restraints weight = 159854.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.062295 restraints weight = 88705.803| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29144 Z= 0.124 Angle : 0.553 12.476 39693 Z= 0.284 Chirality : 0.044 0.263 4482 Planarity : 0.004 0.057 5138 Dihedral : 4.609 55.442 3925 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.99 % Favored : 95.81 % Rotamer: Outliers : 0.03 % Allowed : 1.29 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3605 helix: 0.94 (0.19), residues: 729 sheet: 0.19 (0.17), residues: 888 loop : -0.72 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 50 HIS 0.008 0.001 HIS C1101 PHE 0.021 0.001 PHE C 92 TYR 0.019 0.001 TYR E 248 ARG 0.007 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00022 ( 1) link_NAG-ASN : angle 4.68305 ( 3) hydrogen bonds : bond 0.03611 ( 1081) hydrogen bonds : angle 5.86834 ( 3072) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.43340 ( 84) covalent geometry : bond 0.00277 (29101) covalent geometry : angle 0.54856 (39606) *********************** 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 317 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 3.064 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: 0.2634 (p90) cc_final: 0.1636 (t80) REVERT: E 304 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8267 (tptm) REVERT: E 448 ASN cc_start: 0.6693 (t0) cc_final: 0.5415 (m110) REVERT: E 493 GLN cc_start: 0.8622 (mt0) cc_final: 0.8383 (mp10) REVERT: E 532 ASN cc_start: 0.8557 (m-40) cc_final: 0.8172 (p0) REVERT: E 740 MET cc_start: 0.7685 (tpp) cc_final: 0.7379 (tpp) REVERT: E 754 LEU cc_start: 0.8923 (mm) cc_final: 0.8669 (tt) REVERT: E 864 LEU cc_start: 0.8959 (tp) cc_final: 0.8652 (tp) REVERT: E 1023 ASN cc_start: 0.8873 (m110) cc_final: 0.8483 (m110) REVERT: E 1029 MET cc_start: 0.8847 (mmp) cc_final: 0.7086 (mmp) REVERT: E 1030 SER cc_start: 0.9150 (m) cc_final: 0.8864 (p) REVERT: E 1062 PHE cc_start: 0.8125 (m-10) cc_final: 0.7805 (m-80) REVERT: B 162 ASN cc_start: 0.6958 (m-40) cc_final: 0.6503 (t0) REVERT: C 52 GLN cc_start: 0.9075 (tt0) cc_final: 0.8047 (pm20) REVERT: C 229 LEU cc_start: 0.8549 (mt) cc_final: 0.8299 (mt) REVERT: C 559 PHE cc_start: 0.6396 (m-80) cc_final: 0.5957 (m-80) REVERT: C 721 SER cc_start: 0.9127 (m) cc_final: 0.8824 (t) REVERT: C 732 THR cc_start: 0.8137 (p) cc_final: 0.7909 (p) REVERT: C 773 GLU cc_start: 0.8033 (tp30) cc_final: 0.7601 (tp30) REVERT: C 774 GLN cc_start: 0.8684 (mm-40) cc_final: 0.7209 (mt0) REVERT: C 777 ASN cc_start: 0.8411 (m110) cc_final: 0.6779 (m110) REVERT: C 902 MET cc_start: 0.8863 (mmm) cc_final: 0.8636 (mmp) REVERT: C 921 LYS cc_start: 0.9049 (mttt) cc_final: 0.8805 (pttp) REVERT: C 945 LEU cc_start: 0.7474 (tp) cc_final: 0.7254 (mp) REVERT: C 957 GLN cc_start: 0.8563 (tp-100) cc_final: 0.8247 (tp-100) REVERT: C 1018 ILE cc_start: 0.9269 (mt) cc_final: 0.9012 (tt) REVERT: C 1019 ARG cc_start: 0.9328 (ptt-90) cc_final: 0.8849 (ptt90) REVERT: C 1029 MET cc_start: 0.8397 (tpp) cc_final: 0.8178 (mmp) REVERT: C 1031 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8385 (mt-10) REVERT: D 302 THR cc_start: 0.8685 (m) cc_final: 0.8484 (p) REVERT: D 464 PHE cc_start: 0.8176 (m-80) cc_final: 0.7908 (m-10) REVERT: D 532 ASN cc_start: 0.7716 (m-40) cc_final: 0.7216 (t0) REVERT: D 697 MET cc_start: 0.7484 (mmp) cc_final: 0.6657 (mmp) REVERT: D 742 ILE cc_start: 0.8086 (mt) cc_final: 0.7678 (tp) REVERT: D 774 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8569 (mm-40) REVERT: D 955 ASN cc_start: 0.9161 (t0) cc_final: 0.8955 (t0) REVERT: D 1031 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8447 (mp0) REVERT: D 1089 PHE cc_start: 0.8199 (m-80) cc_final: 0.7983 (m-80) outliers start: 1 outliers final: 1 residues processed: 317 average time/residue: 0.3654 time to fit residues: 191.4751 Evaluate side-chains 222 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 65 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 23 GLN E 245 HIS ** 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 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN C 99 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN D1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.066562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.057008 restraints weight = 285700.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.058203 restraints weight = 160063.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.059000 restraints weight = 100761.999| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.6476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 29144 Z= 0.224 Angle : 0.673 12.462 39693 Z= 0.350 Chirality : 0.046 0.237 4482 Planarity : 0.005 0.053 5138 Dihedral : 5.257 59.819 3925 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.33 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3605 helix: 0.73 (0.20), residues: 725 sheet: -0.02 (0.17), residues: 872 loop : -0.93 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 50 HIS 0.027 0.002 HIS D1048 PHE 0.024 0.002 PHE D 275 TYR 0.027 0.002 TYR D 313 ARG 0.018 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00060 ( 1) link_NAG-ASN : angle 5.74990 ( 3) hydrogen bonds : bond 0.04261 ( 1081) hydrogen bonds : angle 6.28267 ( 3072) SS BOND : bond 0.00486 ( 42) SS BOND : angle 1.52115 ( 84) covalent geometry : bond 0.00482 (29101) covalent geometry : angle 0.66844 (39606) *********************** 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 293 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 3.172 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 175 PHE cc_start: 0.2854 (p90) cc_final: 0.1842 (t80) REVERT: E 304 LYS cc_start: 0.9001 (mmtm) cc_final: 0.8354 (tptp) REVERT: E 340 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7058 (pt0) REVERT: E 360 ASN cc_start: 0.6791 (t0) cc_final: 0.6533 (t0) REVERT: E 532 ASN cc_start: 0.8662 (m-40) cc_final: 0.8269 (p0) REVERT: E 725 GLU cc_start: 0.8496 (tt0) cc_final: 0.8149 (tt0) REVERT: E 740 MET cc_start: 0.7819 (tpp) cc_final: 0.7564 (tpp) REVERT: E 754 LEU cc_start: 0.9060 (mm) cc_final: 0.8825 (tt) REVERT: E 864 LEU cc_start: 0.9008 (tp) cc_final: 0.8757 (tp) REVERT: E 973 ILE cc_start: 0.7857 (mt) cc_final: 0.7631 (mt) REVERT: E 993 ILE cc_start: 0.9204 (mt) cc_final: 0.8916 (mt) REVERT: E 1023 ASN cc_start: 0.8895 (m110) cc_final: 0.8573 (m110) REVERT: E 1030 SER cc_start: 0.9093 (m) cc_final: 0.8753 (p) REVERT: A 78 THR cc_start: 0.7137 (m) cc_final: 0.6935 (m) REVERT: A 177 GLN cc_start: 0.2938 (tp40) cc_final: 0.1925 (pt0) REVERT: C 721 SER cc_start: 0.9170 (m) cc_final: 0.8869 (t) REVERT: C 773 GLU cc_start: 0.8401 (tp30) cc_final: 0.7997 (tp30) REVERT: C 777 ASN cc_start: 0.8496 (m110) cc_final: 0.6877 (m110) REVERT: C 902 MET cc_start: 0.9001 (mmm) cc_final: 0.8678 (mmp) REVERT: C 904 TYR cc_start: 0.8470 (t80) cc_final: 0.8254 (t80) REVERT: C 921 LYS cc_start: 0.9134 (mttt) cc_final: 0.8834 (pttp) REVERT: C 945 LEU cc_start: 0.7984 (tp) cc_final: 0.7672 (mp) REVERT: C 957 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8372 (tp-100) REVERT: C 1019 ARG cc_start: 0.9323 (ptt-90) cc_final: 0.9066 (ptt90) REVERT: C 1029 MET cc_start: 0.8471 (tpp) cc_final: 0.8237 (mmp) REVERT: D 177 MET cc_start: 0.4596 (mpp) cc_final: 0.4327 (mtm) REVERT: D 215 ASP cc_start: 0.8342 (m-30) cc_final: 0.8111 (m-30) REVERT: D 464 PHE cc_start: 0.8406 (m-80) cc_final: 0.8136 (m-10) REVERT: D 532 ASN cc_start: 0.7815 (m-40) cc_final: 0.7352 (t0) REVERT: D 742 ILE cc_start: 0.8159 (mt) cc_final: 0.7884 (tp) REVERT: D 774 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8901 (mm-40) REVERT: D 1031 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8707 (mp0) REVERT: D 1089 PHE cc_start: 0.8340 (m-80) cc_final: 0.8054 (m-80) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.3595 time to fit residues: 174.5536 Evaluate side-chains 209 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 337 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 305 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 189 optimal weight: 30.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 18 GLN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C1002 GLN C1101 HIS ** C1106 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** D1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.067241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.057805 restraints weight = 283764.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.059191 restraints weight = 162575.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.060242 restraints weight = 90545.847| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29144 Z= 0.166 Angle : 0.604 11.858 39693 Z= 0.316 Chirality : 0.045 0.178 4482 Planarity : 0.004 0.059 5138 Dihedral : 5.134 57.487 3925 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.72 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3605 helix: 0.84 (0.20), residues: 714 sheet: -0.12 (0.17), residues: 894 loop : -0.92 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 50 HIS 0.023 0.002 HIS D1048 PHE 0.019 0.002 PHE D 275 TYR 0.022 0.002 TYR E 248 ARG 0.006 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 1) link_NAG-ASN : angle 5.25264 ( 3) hydrogen bonds : bond 0.03907 ( 1081) hydrogen bonds : angle 6.17464 ( 3072) SS BOND : bond 0.00465 ( 42) SS BOND : angle 1.46388 ( 84) covalent geometry : bond 0.00364 (29101) covalent geometry : angle 0.59950 (39606) *********************** 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 283 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 3.094 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 175 PHE cc_start: 0.2463 (p90) cc_final: 0.1508 (t80) REVERT: E 304 LYS cc_start: 0.9051 (mmtm) cc_final: 0.8385 (tptp) REVERT: E 532 ASN cc_start: 0.8522 (m-40) cc_final: 0.8196 (p0) REVERT: E 740 MET cc_start: 0.7432 (tpp) cc_final: 0.7145 (tpp) REVERT: E 864 LEU cc_start: 0.8775 (tp) cc_final: 0.8445 (tp) REVERT: E 1018 ILE cc_start: 0.9461 (mm) cc_final: 0.8510 (mp) REVERT: E 1023 ASN cc_start: 0.8801 (m110) cc_final: 0.8511 (m110) REVERT: E 1027 THR cc_start: 0.9070 (m) cc_final: 0.8781 (p) REVERT: E 1029 MET cc_start: 0.8639 (mmp) cc_final: 0.7048 (mmp) REVERT: E 1030 SER cc_start: 0.9132 (m) cc_final: 0.8768 (p) REVERT: E 1050 MET cc_start: 0.8680 (pmm) cc_final: 0.7958 (pmm) REVERT: A 177 GLN cc_start: 0.3214 (tp40) cc_final: 0.2037 (pt0) REVERT: C 52 GLN cc_start: 0.9252 (tt0) cc_final: 0.8129 (pm20) REVERT: C 559 PHE cc_start: 0.5981 (m-80) cc_final: 0.5392 (m-80) REVERT: C 721 SER cc_start: 0.9060 (m) cc_final: 0.8713 (t) REVERT: C 777 ASN cc_start: 0.8243 (m110) cc_final: 0.6481 (m110) REVERT: C 921 LYS cc_start: 0.9098 (mttt) cc_final: 0.8884 (pttp) REVERT: C 1019 ARG cc_start: 0.9160 (ptt-90) cc_final: 0.8938 (ptt90) REVERT: C 1029 MET cc_start: 0.8300 (tpp) cc_final: 0.8057 (mmp) REVERT: C 1031 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8209 (mm-30) REVERT: D 464 PHE cc_start: 0.8247 (m-80) cc_final: 0.8037 (m-10) REVERT: D 532 ASN cc_start: 0.7699 (m-40) cc_final: 0.7253 (t0) REVERT: D 742 ILE cc_start: 0.8063 (mt) cc_final: 0.7749 (tp) REVERT: D 955 ASN cc_start: 0.9131 (t0) cc_final: 0.8924 (t0) REVERT: D 1118 ASP cc_start: 0.7995 (p0) cc_final: 0.7678 (t70) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3599 time to fit residues: 169.0405 Evaluate side-chains 202 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 120 optimal weight: 10.0000 chunk 359 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 339 optimal weight: 0.7980 chunk 230 optimal weight: 0.5980 chunk 321 optimal weight: 0.5980 chunk 244 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C1002 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 GLN D 953 ASN D1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.068486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.058916 restraints weight = 281428.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.060147 restraints weight = 156803.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.060942 restraints weight = 98180.795| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29144 Z= 0.122 Angle : 0.577 11.686 39693 Z= 0.300 Chirality : 0.044 0.189 4482 Planarity : 0.004 0.075 5138 Dihedral : 4.805 55.895 3925 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.55 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3605 helix: 0.79 (0.19), residues: 725 sheet: -0.07 (0.17), residues: 895 loop : -0.90 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 50 HIS 0.020 0.001 HIS D1048 PHE 0.028 0.002 PHE C1052 TYR 0.028 0.001 TYR E 756 ARG 0.007 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 1) link_NAG-ASN : angle 4.19042 ( 3) hydrogen bonds : bond 0.03709 ( 1081) hydrogen bonds : angle 5.97053 ( 3072) SS BOND : bond 0.00430 ( 42) SS BOND : angle 1.43515 ( 84) covalent geometry : bond 0.00275 (29101) covalent geometry : angle 0.57317 (39606) ********************** 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 301 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 2.981 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: E 175 PHE cc_start: 0.2025 (p90) cc_final: 0.1383 (t80) REVERT: E 304 LYS cc_start: 0.8993 (mmtm) cc_final: 0.8350 (tptp) REVERT: E 360 ASN cc_start: 0.6428 (t0) cc_final: 0.6172 (t0) REVERT: E 493 GLN cc_start: 0.8539 (mt0) cc_final: 0.8316 (mp10) REVERT: E 532 ASN cc_start: 0.8450 (m-40) cc_final: 0.8130 (p0) REVERT: E 740 MET cc_start: 0.7577 (tpp) cc_final: 0.7273 (tpp) REVERT: E 1023 ASN cc_start: 0.8818 (m110) cc_final: 0.8521 (m110) REVERT: E 1030 SER cc_start: 0.9080 (m) cc_final: 0.8710 (p) REVERT: E 1050 MET cc_start: 0.8661 (pmm) cc_final: 0.8001 (pmm) REVERT: A 177 GLN cc_start: 0.3205 (tp40) cc_final: 0.2086 (pt0) REVERT: C 52 GLN cc_start: 0.9186 (tt0) cc_final: 0.8164 (pm20) REVERT: C 559 PHE cc_start: 0.6067 (m-80) cc_final: 0.5444 (m-80) REVERT: C 721 SER cc_start: 0.9078 (m) cc_final: 0.8770 (p) REVERT: C 740 MET cc_start: 0.7634 (ptt) cc_final: 0.7332 (ptt) REVERT: C 777 ASN cc_start: 0.7580 (m110) cc_final: 0.7125 (m110) REVERT: C 902 MET cc_start: 0.8820 (mmm) cc_final: 0.8578 (mmp) REVERT: C 904 TYR cc_start: 0.8542 (t80) cc_final: 0.8341 (t80) REVERT: C 921 LYS cc_start: 0.9087 (mttt) cc_final: 0.8858 (pttp) REVERT: D 153 MET cc_start: 0.6209 (pmm) cc_final: 0.5954 (pmm) REVERT: D 177 MET cc_start: 0.3083 (mtm) cc_final: 0.1817 (mmt) REVERT: D 532 ASN cc_start: 0.7641 (m-40) cc_final: 0.7187 (t0) REVERT: D 742 ILE cc_start: 0.8080 (mt) cc_final: 0.7707 (tp) REVERT: D 954 GLN cc_start: 0.8580 (tm-30) cc_final: 0.7966 (tm-30) REVERT: D 1089 PHE cc_start: 0.8095 (m-80) cc_final: 0.7774 (m-80) REVERT: D 1118 ASP cc_start: 0.7992 (p0) cc_final: 0.7675 (t70) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.3541 time to fit residues: 177.0642 Evaluate side-chains 207 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 106 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 314 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1011 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** D1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.065834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.056486 restraints weight = 283979.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.057851 restraints weight = 163702.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.058986 restraints weight = 91226.427| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29144 Z= 0.236 Angle : 0.687 11.854 39693 Z= 0.359 Chirality : 0.046 0.193 4482 Planarity : 0.005 0.098 5138 Dihedral : 5.329 59.921 3925 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.69 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3605 helix: 0.73 (0.19), residues: 732 sheet: -0.28 (0.17), residues: 876 loop : -1.10 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A 50 HIS 0.018 0.002 HIS D1048 PHE 0.032 0.002 PHE C1052 TYR 0.024 0.002 TYR D 313 ARG 0.007 0.001 ARG D1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00025 ( 1) link_NAG-ASN : angle 5.39855 ( 3) hydrogen bonds : bond 0.04286 ( 1081) hydrogen bonds : angle 6.32893 ( 3072) SS BOND : bond 0.00507 ( 42) SS BOND : angle 1.43235 ( 84) covalent geometry : bond 0.00506 (29101) covalent geometry : angle 0.68277 (39606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9263.16 seconds wall clock time: 163 minutes 25.93 seconds (9805.93 seconds total)