Starting phenix.real_space_refine on Tue Jun 24 17:15:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k9b_36983/06_2025/8k9b_36983.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9b_36983/06_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_36983/06_2025/8k9b_36983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9b_36983/06_2025/8k9b_36983.map" model { file = "/net/cci-nas-00/data/ceres_data/8k9b_36983/06_2025/8k9b_36983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9b_36983/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.01, per 1000 atoms: 0.63 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: 6.87 Conformation dependent library (CDL) restraints added in 3.5 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: 4.21 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: 14.58 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9208 1.34 - 1.46: 7103 1.46 - 1.58: 12625 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 29101 Sorted by residual: bond pdb=" C1 NAG E1301 " pdb=" O5 NAG E1301 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" N ASP B 1 " pdb=" CA ASP B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N GLN E 14 " pdb=" CA GLN E 14 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N GLN D 14 " pdb=" CA GLN D 14 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N GLU A 1 " pdb=" CA GLU A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 ... (remaining 29096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 38641 1.10 - 2.20: 721 2.20 - 3.29: 160 3.29 - 4.39: 76 4.39 - 5.49: 8 Bond angle restraints: 39606 Sorted by residual: angle pdb=" C ARG C 21 " pdb=" CA ARG C 21 " pdb=" CB ARG C 21 " ideal model delta sigma weight residual 115.79 111.09 4.70 1.19e+00 7.06e-01 1.56e+01 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 111.56 108.31 3.25 8.60e-01 1.35e+00 1.43e+01 angle pdb=" N ILE C 666 " pdb=" CA ILE C 666 " pdb=" C ILE C 666 " ideal model delta sigma weight residual 111.62 108.82 2.80 7.90e-01 1.60e+00 1.25e+01 angle pdb=" N ILE E 666 " pdb=" CA ILE E 666 " pdb=" C ILE E 666 " ideal model delta sigma weight residual 111.56 108.59 2.97 8.60e-01 1.35e+00 1.19e+01 angle pdb=" N VAL D 341 " pdb=" CA VAL D 341 " pdb=" C VAL D 341 " ideal model delta sigma weight residual 111.62 109.02 2.60 7.90e-01 1.60e+00 1.09e+01 ... (remaining 39601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 16857 16.94 - 33.87: 391 33.87 - 50.81: 93 50.81 - 67.75: 25 67.75 - 84.68: 8 Dihedral angle restraints: 17374 sinusoidal: 6773 harmonic: 10601 Sorted by residual: dihedral pdb=" CA ASN E 148 " pdb=" C ASN E 148 " pdb=" N ASN E 149 " pdb=" CA ASN E 149 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CB CYS A 146 " pdb=" SG CYS A 146 " pdb=" SG CYS A 201 " pdb=" CB CYS A 201 " ideal model delta sinusoidal sigma weight residual 93.00 53.93 39.07 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 61.12 31.88 1 1.00e+01 1.00e-02 1.45e+01 ... (remaining 17371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2835 0.029 - 0.057: 1110 0.057 - 0.086: 138 0.086 - 0.115: 302 0.115 - 0.143: 97 Chirality restraints: 4482 Sorted by residual: chirality pdb=" CA ILE E 714 " pdb=" N ILE E 714 " pdb=" C ILE E 714 " pdb=" CB ILE E 714 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE D 714 " pdb=" N ILE D 714 " pdb=" C ILE D 714 " pdb=" CB ILE D 714 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE C 664 " pdb=" N ILE C 664 " pdb=" C ILE C 664 " pdb=" CB ILE C 664 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 4479 not shown) Planarity restraints: 5139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 916 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C LEU E 916 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU E 916 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR E 917 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 986 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO E 987 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 987 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 987 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 61 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 62 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " 0.017 5.00e-02 4.00e+02 ... (remaining 5136 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 195 2.57 - 3.16: 23448 3.16 - 3.74: 42621 3.74 - 4.32: 60796 4.32 - 4.90: 102793 Nonbonded interactions: 229853 Sorted by model distance: nonbonded pdb=" OH TYR D 756 " pdb=" OD1 ASP D 994 " model vdw 1.993 3.040 nonbonded pdb=" OH TYR E 756 " pdb=" OD1 ASP E 994 " model vdw 1.999 3.040 nonbonded pdb=" OG SER C 383 " pdb=" OD1 ASP D 985 " model vdw 2.012 3.040 nonbonded pdb=" OD1 ASP E 985 " pdb=" OG SER D 383 " model vdw 2.014 3.040 nonbonded pdb=" OG SER E 813 " pdb=" OE1 GLU E 868 " model vdw 2.024 3.040 ... (remaining 229848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 16 through 827 or resid 849 through 1147)) selection = (chain 'E' and (resid 16 through 247 or resid 255 through 827 or resid 849 throu \ gh 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.420 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: 0.060 Extract box with map and model: 1.200 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 68.770 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.210 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.960 ------------------------------------------------------------------------------- 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 : 3.468 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: 0.4542 time to fit residues: 589.2760 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 : 3.072 ------------------------------------------------------------------------------- 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 = 54)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.059739 restraints weight = 282619.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.060938 restraints weight = 159381.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.061647 restraints weight = 101332.638| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 6.40371 ( 3) hydrogen bonds : bond 0.05435 ( 1081) hydrogen bonds : angle 6.99412 ( 3072) SS BOND : bond 0.00646 ( 42) SS BOND : angle 1.42178 ( 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 : 3.117 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: 0.8371 (tptm) REVERT: E 493 GLN cc_start: 0.8683 (mt0) cc_final: 0.8349 (mp10) REVERT: E 532 ASN cc_start: 0.8385 (m-40) cc_final: 0.8057 (p0) REVERT: E 818 ILE cc_start: 0.8948 (mt) cc_final: 0.8547 (mt) REVERT: E 864 LEU cc_start: 0.9023 (tp) cc_final: 0.8770 (tp) REVERT: E 1029 MET cc_start: 0.8721 (tpp) cc_final: 0.8342 (mmm) REVERT: E 1033 VAL cc_start: 0.8671 (t) cc_final: 0.7549 (t) REVERT: E 1047 TYR cc_start: 0.8323 (m-80) cc_final: 0.8054 (m-10) REVERT: E 1062 PHE cc_start: 0.8649 (m-10) cc_final: 0.8248 (m-80) REVERT: A 63 LYS cc_start: 0.7281 (mttt) cc_final: 0.7000 (tttt) REVERT: A 214 LYS cc_start: 0.3131 (mmmt) cc_final: 0.2536 (tptt) REVERT: B 58 ASN cc_start: 0.3968 (m-40) cc_final: 0.3682 (m-40) REVERT: B 162 ASN cc_start: 0.6367 (m-40) cc_final: 0.6085 (t0) REVERT: C 52 GLN cc_start: 0.9173 (tt0) cc_final: 0.8087 (pm20) REVERT: C 58 PHE cc_start: 0.7507 (m-10) cc_final: 0.7267 (m-10) REVERT: C 269 TYR cc_start: 0.7362 (m-10) cc_final: 0.7027 (m-80) REVERT: C 314 GLN cc_start: 0.7986 (tt0) cc_final: 0.7747 (tm-30) REVERT: C 772 VAL cc_start: 0.9254 (t) cc_final: 0.9038 (p) REVERT: C 854 LYS cc_start: 0.3047 (pttt) cc_final: 0.2801 (pttt) REVERT: C 904 TYR cc_start: 0.8743 (t80) cc_final: 0.8416 (t80) REVERT: C 1001 LEU cc_start: 0.9160 (tp) cc_final: 0.8899 (tt) REVERT: C 1013 ILE cc_start: 0.9636 (mt) cc_final: 0.9237 (mt) REVERT: C 1017 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8808 (pm20) REVERT: C 1018 ILE cc_start: 0.9374 (mt) cc_final: 0.9121 (tt) REVERT: C 1031 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8018 (mt-10) REVERT: C 1052 PHE cc_start: 0.8653 (m-10) cc_final: 0.8230 (m-10) REVERT: D 302 THR cc_start: 0.8718 (m) cc_final: 0.8442 (p) REVERT: D 455 LEU cc_start: 0.7922 (tp) cc_final: 0.7647 (tp) REVERT: D 464 PHE cc_start: 0.8161 (m-80) cc_final: 0.7756 (m-10) REVERT: D 532 ASN cc_start: 0.7587 (m-40) cc_final: 0.7248 (t0) REVERT: D 697 MET cc_start: 0.7909 (ttm) cc_final: 0.7682 (mtp) REVERT: D 723 THR cc_start: 0.8926 (m) cc_final: 0.8673 (p) REVERT: D 731 MET cc_start: 0.8855 (ttp) cc_final: 0.8232 (ttm) REVERT: D 774 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8951 (mm110) REVERT: D 817 PHE cc_start: 0.7993 (t80) cc_final: 0.7792 (t80) REVERT: D 875 SER cc_start: 0.8957 (t) cc_final: 0.8706 (p) REVERT: D 904 TYR cc_start: 0.8433 (t80) cc_final: 0.7822 (t80) REVERT: D 1019 ARG cc_start: 0.8096 (tmt170) cc_final: 0.7843 (ttp80) REVERT: D 1029 MET cc_start: 0.8608 (tmm) cc_final: 0.8281 (tmm) outliers start: 6 outliers final: 1 residues processed: 441 average time/residue: 0.4475 time to fit residues: 310.9509 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 : 3.021 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 303 optimal weight: 0.0030 chunk 32 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 208 optimal weight: 0.0570 chunk 202 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 overall best weight: 0.7910 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.071241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.061526 restraints weight = 279679.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.062743 restraints weight = 157103.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.063606 restraints weight = 99614.372| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29144 Z= 0.137 Angle : 0.572 11.342 39693 Z= 0.298 Chirality : 0.044 0.168 4482 Planarity : 0.004 0.070 5138 Dihedral : 4.468 57.087 3925 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.94 % Favored : 96.87 % Rotamer: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % 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: 0.09 (0.13), residues: 3605 helix: 1.15 (0.19), residues: 719 sheet: 0.42 (0.16), residues: 931 loop : -0.49 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 50 HIS 0.006 0.001 HIS C1101 PHE 0.044 0.002 PHE E 342 TYR 0.024 0.002 TYR E 873 ARG 0.007 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 1) link_NAG-ASN : angle 4.77060 ( 3) hydrogen bonds : bond 0.04083 ( 1081) hydrogen bonds : angle 6.27034 ( 3072) SS BOND : bond 0.00365 ( 42) SS BOND : angle 1.34947 ( 84) covalent geometry : bond 0.00297 (29101) covalent geometry : angle 0.56723 (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 390 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 3.215 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: E 193 VAL cc_start: 0.8922 (t) cc_final: 0.8718 (t) REVERT: E 194 PHE cc_start: 0.6647 (m-80) cc_final: 0.6296 (m-80) REVERT: E 340 GLU cc_start: 0.8301 (pt0) cc_final: 0.7776 (pp20) REVERT: E 490 PHE cc_start: 0.2358 (t80) cc_final: 0.2149 (t80) REVERT: E 493 GLN cc_start: 0.8766 (mt0) cc_final: 0.8496 (mp10) REVERT: E 532 ASN cc_start: 0.8379 (m-40) cc_final: 0.8010 (p0) REVERT: E 740 MET cc_start: 0.7916 (tpp) cc_final: 0.7668 (tpp) REVERT: E 864 LEU cc_start: 0.9012 (tp) cc_final: 0.8599 (tp) REVERT: E 945 LEU cc_start: 0.8982 (pp) cc_final: 0.8628 (pp) REVERT: E 949 GLN cc_start: 0.8253 (mm110) cc_final: 0.7927 (mm-40) REVERT: E 1023 ASN cc_start: 0.8817 (m110) cc_final: 0.8461 (m110) REVERT: E 1033 VAL cc_start: 0.8620 (t) cc_final: 0.7944 (t) REVERT: A 63 LYS cc_start: 0.7125 (mttt) cc_final: 0.6844 (tttt) REVERT: A 214 LYS cc_start: 0.3220 (mmmt) cc_final: 0.2573 (tptp) REVERT: B 58 ASN cc_start: 0.4172 (m-40) cc_final: 0.3832 (m-40) REVERT: B 162 ASN cc_start: 0.6259 (m-40) cc_final: 0.6024 (t0) REVERT: B 168 TRP cc_start: 0.3639 (t60) cc_final: 0.3424 (t60) REVERT: C 269 TYR cc_start: 0.7318 (m-10) cc_final: 0.6992 (m-10) REVERT: C 697 MET cc_start: 0.7883 (mtp) cc_final: 0.7663 (mtp) REVERT: C 752 LEU cc_start: 0.8867 (mt) cc_final: 0.7894 (tp) REVERT: C 904 TYR cc_start: 0.8778 (t80) cc_final: 0.8333 (t80) REVERT: C 957 GLN cc_start: 0.8468 (tp-100) cc_final: 0.8232 (tp-100) REVERT: C 962 LEU cc_start: 0.9054 (tp) cc_final: 0.8803 (tp) REVERT: C 1018 ILE cc_start: 0.9251 (mt) cc_final: 0.8896 (tt) REVERT: C 1052 PHE cc_start: 0.8697 (m-10) cc_final: 0.8399 (m-10) REVERT: C 1055 SER cc_start: 0.8189 (t) cc_final: 0.7989 (t) REVERT: D 302 THR cc_start: 0.8673 (m) cc_final: 0.8453 (p) REVERT: D 464 PHE cc_start: 0.7965 (m-80) cc_final: 0.7643 (m-10) REVERT: D 492 LEU cc_start: 0.8134 (mp) cc_final: 0.7836 (tp) REVERT: D 532 ASN cc_start: 0.7531 (m-40) cc_final: 0.7166 (t0) REVERT: D 723 THR cc_start: 0.8855 (m) cc_final: 0.8600 (p) REVERT: D 742 ILE cc_start: 0.7831 (mt) cc_final: 0.7547 (tp) REVERT: D 774 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8919 (mm-40) REVERT: D 904 TYR cc_start: 0.8433 (t80) cc_final: 0.8221 (t80) REVERT: D 909 ILE cc_start: 0.8944 (pt) cc_final: 0.8698 (mt) REVERT: D 1031 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8298 (mp0) REVERT: D 1089 PHE cc_start: 0.8148 (m-80) cc_final: 0.7763 (m-80) outliers start: 1 outliers final: 0 residues processed: 390 average time/residue: 0.3942 time to fit residues: 245.2896 Evaluate side-chains 256 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 2.925 ------------------------------------------------------------------------------- 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: 0.0870 chunk 122 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 302 optimal weight: 9.9990 chunk 34 optimal weight: 0.4980 chunk 186 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 304 optimal weight: 0.1980 chunk 45 optimal weight: 10.0000 overall best weight: 0.5160 ------------------------------------------------------------------------------- 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 955 ASN ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN C 394 ASN C 613 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN D 644 GLN D 777 ASN D 856 ASN D1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.063917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.052208 restraints weight = 229740.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.053442 restraints weight = 143287.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.054302 restraints weight = 98929.667| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29144 Z= 0.118 Angle : 0.538 11.363 39693 Z= 0.278 Chirality : 0.043 0.195 4482 Planarity : 0.004 0.050 5138 Dihedral : 4.311 58.319 3925 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.16 % Favored : 96.67 % Rotamer: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.30 % 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: 0.06 (0.13), residues: 3605 helix: 1.11 (0.20), residues: 711 sheet: 0.49 (0.16), residues: 910 loop : -0.55 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 50 HIS 0.006 0.001 HIS C1101 PHE 0.022 0.001 PHE D 855 TYR 0.021 0.001 TYR E 873 ARG 0.008 0.000 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 1) link_NAG-ASN : angle 4.37350 ( 3) hydrogen bonds : bond 0.03708 ( 1081) hydrogen bonds : angle 6.01424 ( 3072) SS BOND : bond 0.00540 ( 42) SS BOND : angle 1.24660 ( 84) covalent geometry : bond 0.00261 (29101) covalent geometry : angle 0.53464 (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 370 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 3.084 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: E 304 LYS cc_start: 0.8876 (mmtm) cc_final: 0.8324 (tptm) REVERT: E 493 GLN cc_start: 0.8666 (mt0) cc_final: 0.8397 (mp10) REVERT: E 532 ASN cc_start: 0.8524 (m-40) cc_final: 0.8076 (p0) REVERT: E 740 MET cc_start: 0.7792 (tpp) cc_final: 0.7587 (tpp) REVERT: E 754 LEU cc_start: 0.8875 (mm) cc_final: 0.8461 (tt) REVERT: E 864 LEU cc_start: 0.8809 (tp) cc_final: 0.8472 (tp) REVERT: E 950 ASP cc_start: 0.8854 (t0) cc_final: 0.7890 (t0) REVERT: E 1023 ASN cc_start: 0.8836 (m110) cc_final: 0.8494 (m110) REVERT: E 1029 MET cc_start: 0.8608 (mmp) cc_final: 0.7087 (mmp) REVERT: E 1030 SER cc_start: 0.9204 (m) cc_final: 0.8962 (p) REVERT: A 63 LYS cc_start: 0.6956 (mttt) cc_final: 0.6625 (tttt) REVERT: A 214 LYS cc_start: 0.3162 (mmmt) cc_final: 0.2549 (tptp) REVERT: B 58 ASN cc_start: 0.4069 (m-40) cc_final: 0.3728 (m-40) REVERT: B 162 ASN cc_start: 0.6729 (m-40) cc_final: 0.6328 (t0) REVERT: B 178 TYR cc_start: 0.6980 (m-10) cc_final: 0.6544 (m-10) REVERT: C 269 TYR cc_start: 0.7536 (m-10) cc_final: 0.7186 (m-10) REVERT: C 752 LEU cc_start: 0.8814 (mt) cc_final: 0.7879 (tp) REVERT: C 773 GLU cc_start: 0.7958 (tp30) cc_final: 0.7599 (tp30) REVERT: C 823 PHE cc_start: 0.7661 (m-10) cc_final: 0.7375 (m-10) REVERT: C 904 TYR cc_start: 0.8627 (t80) cc_final: 0.8235 (t80) REVERT: C 945 LEU cc_start: 0.7782 (tt) cc_final: 0.7215 (mp) REVERT: C 950 ASP cc_start: 0.8501 (m-30) cc_final: 0.8197 (t0) REVERT: C 957 GLN cc_start: 0.8341 (tp-100) cc_final: 0.8123 (tp-100) REVERT: C 962 LEU cc_start: 0.9031 (tp) cc_final: 0.8783 (tp) REVERT: C 1018 ILE cc_start: 0.9121 (mt) cc_final: 0.8706 (tt) REVERT: C 1031 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8056 (mt-10) REVERT: D 302 THR cc_start: 0.8625 (m) cc_final: 0.8205 (p) REVERT: D 304 LYS cc_start: 0.9308 (mptt) cc_final: 0.8976 (mmtt) REVERT: D 464 PHE cc_start: 0.7990 (m-80) cc_final: 0.7670 (m-10) REVERT: D 492 LEU cc_start: 0.8330 (mp) cc_final: 0.8080 (tp) REVERT: D 532 ASN cc_start: 0.7787 (m-40) cc_final: 0.7295 (t0) REVERT: D 912 THR cc_start: 0.8745 (m) cc_final: 0.8426 (m) REVERT: D 1004 LEU cc_start: 0.8953 (mt) cc_final: 0.8659 (mt) REVERT: D 1089 PHE cc_start: 0.8405 (m-80) cc_final: 0.7913 (m-80) outliers start: 2 outliers final: 1 residues processed: 369 average time/residue: 0.3902 time to fit residues: 233.4557 Evaluate side-chains 251 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 3.032 ------------------------------------------------------------------------------- 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: 4.9990 chunk 68 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 258 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 895 GLN ** E 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 957 GLN ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN B 142 ASN B 194 HIS C 542 ASN ** 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.062725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.051128 restraints weight = 240614.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.052382 restraints weight = 148326.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.053243 restraints weight = 101041.023| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 29144 Z= 0.168 Angle : 0.576 12.782 39693 Z= 0.299 Chirality : 0.044 0.193 4482 Planarity : 0.004 0.050 5138 Dihedral : 4.514 59.177 3925 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.91 % Favored : 95.89 % Rotamer: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % 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: -0.06 (0.13), residues: 3605 helix: 1.05 (0.20), residues: 717 sheet: 0.32 (0.16), residues: 908 loop : -0.59 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 50 HIS 0.007 0.001 HIS C1101 PHE 0.034 0.002 PHE C 797 TYR 0.034 0.002 TYR E1047 ARG 0.007 0.001 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 4.94270 ( 3) hydrogen bonds : bond 0.03795 ( 1081) hydrogen bonds : angle 6.04779 ( 3072) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.32636 ( 84) covalent geometry : bond 0.00369 (29101) covalent geometry : angle 0.57181 (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 333 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 time to evaluate : 3.007 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 493 GLN cc_start: 0.8703 (mt0) cc_final: 0.8495 (mp10) REVERT: E 532 ASN cc_start: 0.8545 (m-40) cc_final: 0.8142 (p0) REVERT: E 562 PHE cc_start: 0.7522 (m-80) cc_final: 0.7310 (m-80) REVERT: E 740 MET cc_start: 0.7886 (tpp) cc_final: 0.7662 (tpp) REVERT: E 752 LEU cc_start: 0.8740 (mm) cc_final: 0.8238 (mt) REVERT: E 754 LEU cc_start: 0.8889 (mm) cc_final: 0.8534 (tt) REVERT: E 864 LEU cc_start: 0.8986 (tp) cc_final: 0.8678 (tp) REVERT: E 973 ILE cc_start: 0.7771 (mt) cc_final: 0.7541 (mt) REVERT: E 1023 ASN cc_start: 0.8859 (m110) cc_final: 0.8506 (m110) REVERT: E 1030 SER cc_start: 0.9241 (m) cc_final: 0.8827 (p) REVERT: E 1050 MET cc_start: 0.8684 (pmm) cc_final: 0.8232 (pmm) REVERT: E 1062 PHE cc_start: 0.8411 (m-80) cc_final: 0.7940 (m-80) REVERT: A 214 LYS cc_start: 0.3228 (mmmt) cc_final: 0.2636 (tptp) REVERT: B 58 ASN cc_start: 0.4210 (m-40) cc_final: 0.3962 (m-40) REVERT: B 162 ASN cc_start: 0.6839 (m-40) cc_final: 0.6430 (t0) REVERT: C 52 GLN cc_start: 0.9130 (tt0) cc_final: 0.8012 (pm20) REVERT: C 229 LEU cc_start: 0.8694 (mt) cc_final: 0.8489 (mt) REVERT: C 269 TYR cc_start: 0.7506 (m-10) cc_final: 0.7194 (m-10) REVERT: C 752 LEU cc_start: 0.8973 (mt) cc_final: 0.8071 (tp) REVERT: C 773 GLU cc_start: 0.8094 (tp30) cc_final: 0.7677 (tp30) REVERT: C 777 ASN cc_start: 0.8358 (m-40) cc_final: 0.6652 (m-40) REVERT: C 904 TYR cc_start: 0.8677 (t80) cc_final: 0.8383 (t80) REVERT: C 957 GLN cc_start: 0.8503 (tp-100) cc_final: 0.8235 (tp-100) REVERT: C 962 LEU cc_start: 0.9157 (tp) cc_final: 0.8889 (tp) REVERT: C 988 GLU cc_start: 0.8463 (mp0) cc_final: 0.8209 (mp0) REVERT: C 1018 ILE cc_start: 0.9186 (mt) cc_final: 0.8764 (tt) REVERT: C 1031 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8144 (mt-10) REVERT: D 302 THR cc_start: 0.8716 (m) cc_final: 0.8476 (p) REVERT: D 464 PHE cc_start: 0.7982 (m-80) cc_final: 0.7691 (m-10) REVERT: D 492 LEU cc_start: 0.8131 (mp) cc_final: 0.7844 (tp) REVERT: D 532 ASN cc_start: 0.7846 (m-40) cc_final: 0.7335 (t0) REVERT: D 742 ILE cc_start: 0.8044 (mt) cc_final: 0.7710 (tp) REVERT: D 774 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8444 (mm-40) REVERT: D 1089 PHE cc_start: 0.8418 (m-80) cc_final: 0.7951 (m-80) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.3885 time to fit residues: 211.2642 Evaluate side-chains 224 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 3.027 ------------------------------------------------------------------------------- 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: 0.9980 chunk 278 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 303 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 23 GLN E 115 GLN E 394 ASN ** E 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 27 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** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 751 ASN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.060716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.049791 restraints weight = 251513.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.050997 restraints weight = 153506.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.051877 restraints weight = 103834.687| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29144 Z= 0.239 Angle : 0.698 12.392 39693 Z= 0.365 Chirality : 0.047 0.240 4482 Planarity : 0.005 0.086 5138 Dihedral : 5.260 59.704 3925 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.85 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: -0.50 (0.13), residues: 3605 helix: 0.61 (0.19), residues: 727 sheet: 0.06 (0.17), residues: 882 loop : -0.86 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 50 HIS 0.010 0.002 HIS C1101 PHE 0.028 0.002 PHE C 559 TYR 0.028 0.002 TYR D 313 ARG 0.009 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 1) link_NAG-ASN : angle 5.87663 ( 3) hydrogen bonds : bond 0.04384 ( 1081) hydrogen bonds : angle 6.35028 ( 3072) SS BOND : bond 0.00483 ( 42) SS BOND : angle 1.49388 ( 84) covalent geometry : bond 0.00510 (29101) covalent geometry : angle 0.69374 (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 300 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 3.174 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: 0.9006 (mmtm) cc_final: 0.8388 (tptp) REVERT: E 493 GLN cc_start: 0.8584 (mt0) cc_final: 0.8334 (mp10) REVERT: E 532 ASN cc_start: 0.8676 (m-40) cc_final: 0.8266 (p0) REVERT: E 562 PHE cc_start: 0.7565 (m-80) cc_final: 0.7348 (m-80) REVERT: E 725 GLU cc_start: 0.8256 (tt0) cc_final: 0.7934 (tt0) REVERT: E 740 MET cc_start: 0.7995 (tpp) cc_final: 0.7735 (tpp) REVERT: E 864 LEU cc_start: 0.9041 (tp) cc_final: 0.8818 (tp) REVERT: E 973 ILE cc_start: 0.7859 (mt) cc_final: 0.7603 (mt) REVERT: E 1023 ASN cc_start: 0.8935 (m110) cc_final: 0.8585 (m110) REVERT: E 1027 THR cc_start: 0.9142 (m) cc_final: 0.8855 (p) REVERT: E 1030 SER cc_start: 0.9304 (m) cc_final: 0.8505 (p) REVERT: E 1050 MET cc_start: 0.8682 (pmm) cc_final: 0.7932 (pmm) REVERT: A 177 GLN cc_start: 0.2438 (tp40) cc_final: 0.1515 (pt0) REVERT: B 145 TYR cc_start: 0.5291 (t80) cc_final: 0.4752 (t80) REVERT: B 162 ASN cc_start: 0.6877 (m-40) cc_final: 0.6461 (t0) REVERT: C 731 MET cc_start: 0.7971 (ttm) cc_final: 0.7674 (ttm) REVERT: C 773 GLU cc_start: 0.8500 (tp30) cc_final: 0.8019 (tp30) REVERT: C 777 ASN cc_start: 0.8535 (m-40) cc_final: 0.7390 (m-40) REVERT: C 904 TYR cc_start: 0.8748 (t80) cc_final: 0.8460 (t80) REVERT: C 921 LYS cc_start: 0.9028 (mttt) cc_final: 0.8798 (pttp) REVERT: C 945 LEU cc_start: 0.8133 (tt) cc_final: 0.7513 (mt) REVERT: C 957 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8380 (tp-100) REVERT: C 1006 THR cc_start: 0.9367 (p) cc_final: 0.9121 (p) REVERT: C 1019 ARG cc_start: 0.9171 (pmt-80) cc_final: 0.8910 (pmt-80) REVERT: D 215 ASP cc_start: 0.8163 (m-30) cc_final: 0.7955 (m-30) REVERT: D 532 ASN cc_start: 0.7891 (m-40) cc_final: 0.7339 (t0) REVERT: D 731 MET cc_start: 0.9067 (ttp) cc_final: 0.8798 (ttm) REVERT: D 742 ILE cc_start: 0.8126 (mt) cc_final: 0.7811 (tp) REVERT: D 1001 LEU cc_start: 0.9552 (mt) cc_final: 0.9192 (mt) REVERT: D 1005 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8859 (pt0) REVERT: D 1010 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8938 (tp40) REVERT: D 1089 PHE cc_start: 0.8272 (m-80) cc_final: 0.7951 (m-80) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.3665 time to fit residues: 182.6693 Evaluate side-chains 206 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 3.549 ------------------------------------------------------------------------------- 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: 0.4980 chunk 244 optimal weight: 3.9990 chunk 346 optimal weight: 0.9990 chunk 319 optimal weight: 7.9990 chunk 276 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 299 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 76 optimal weight: 0.0040 chunk 279 optimal weight: 4.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 23 GLN E 149 ASN ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 GLN D 953 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.061819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.050573 restraints weight = 247839.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.051853 restraints weight = 150522.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.052771 restraints weight = 101120.449| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29144 Z= 0.144 Angle : 0.583 12.132 39693 Z= 0.302 Chirality : 0.044 0.224 4482 Planarity : 0.004 0.078 5138 Dihedral : 4.915 56.617 3925 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.94 % Favored : 95.87 % Rotamer: Outliers : 0.09 % Allowed : 1.13 % Favored : 98.78 % 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: -0.42 (0.13), residues: 3605 helix: 0.79 (0.19), residues: 730 sheet: 0.05 (0.17), residues: 895 loop : -0.82 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 50 HIS 0.022 0.001 HIS D1048 PHE 0.029 0.002 PHE D 275 TYR 0.018 0.002 TYR E 248 ARG 0.014 0.001 ARG D1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00014 ( 1) link_NAG-ASN : angle 5.14129 ( 3) hydrogen bonds : bond 0.03787 ( 1081) hydrogen bonds : angle 6.11702 ( 3072) SS BOND : bond 0.00398 ( 42) SS BOND : angle 1.42979 ( 84) covalent geometry : bond 0.00317 (29101) covalent geometry : angle 0.57828 (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 318 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 315 time to evaluate : 3.002 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: 0.2538 (p90) cc_final: 0.1620 (t80) REVERT: E 287 ASP cc_start: 0.8780 (m-30) cc_final: 0.8547 (m-30) REVERT: E 304 LYS cc_start: 0.9019 (mmtm) cc_final: 0.8383 (tptm) REVERT: E 493 GLN cc_start: 0.8575 (mt0) cc_final: 0.8352 (mp10) REVERT: E 532 ASN cc_start: 0.8588 (m-40) cc_final: 0.8205 (p0) REVERT: E 562 PHE cc_start: 0.7514 (m-80) cc_final: 0.7274 (m-80) REVERT: E 740 MET cc_start: 0.7838 (tpp) cc_final: 0.7514 (tpp) REVERT: E 754 LEU cc_start: 0.9045 (mm) cc_final: 0.8736 (tt) REVERT: E 864 LEU cc_start: 0.8959 (tp) cc_final: 0.8729 (tp) REVERT: E 973 ILE cc_start: 0.7805 (mt) cc_final: 0.7557 (mt) REVERT: E 1023 ASN cc_start: 0.8855 (m110) cc_final: 0.8565 (m110) REVERT: E 1027 THR cc_start: 0.9126 (m) cc_final: 0.8808 (p) REVERT: E 1030 SER cc_start: 0.9197 (m) cc_final: 0.8176 (p) REVERT: A 177 GLN cc_start: 0.2528 (tp40) cc_final: 0.1562 (pt0) REVERT: B 145 TYR cc_start: 0.5151 (t80) cc_final: 0.4497 (t80) REVERT: C 52 GLN cc_start: 0.9229 (tt0) cc_final: 0.8183 (pm20) REVERT: C 613 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: C 752 LEU cc_start: 0.9218 (mt) cc_final: 0.8970 (tp) REVERT: C 773 GLU cc_start: 0.8358 (tp30) cc_final: 0.7943 (tp30) REVERT: C 777 ASN cc_start: 0.8402 (m-40) cc_final: 0.6912 (m-40) REVERT: C 904 TYR cc_start: 0.8622 (t80) cc_final: 0.8358 (t80) REVERT: C 921 LYS cc_start: 0.9054 (mttt) cc_final: 0.8823 (pttp) REVERT: C 954 GLN cc_start: 0.9311 (tp-100) cc_final: 0.8987 (tp40) REVERT: C 957 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8334 (tp-100) REVERT: C 1019 ARG cc_start: 0.9123 (pmt-80) cc_final: 0.8639 (pmt-80) REVERT: C 1031 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8249 (mm-30) REVERT: D 215 ASP cc_start: 0.8173 (m-30) cc_final: 0.7947 (m-30) REVERT: D 229 LEU cc_start: 0.9151 (mt) cc_final: 0.8951 (mt) REVERT: D 532 ASN cc_start: 0.7866 (m-40) cc_final: 0.7353 (t0) REVERT: D 697 MET cc_start: 0.7483 (mmp) cc_final: 0.7131 (mmp) REVERT: D 731 MET cc_start: 0.9035 (ttp) cc_final: 0.8795 (ttm) REVERT: D 742 ILE cc_start: 0.8102 (mt) cc_final: 0.7716 (tp) REVERT: D 773 GLU cc_start: 0.8777 (tt0) cc_final: 0.8572 (tt0) REVERT: D 1031 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8496 (mp0) REVERT: D 1089 PHE cc_start: 0.8182 (m-80) cc_final: 0.7957 (m-80) outliers start: 3 outliers final: 1 residues processed: 318 average time/residue: 0.3583 time to fit residues: 188.9044 Evaluate side-chains 221 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 2.907 ------------------------------------------------------------------------------- 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: 1.9990 chunk 143 optimal weight: 0.8980 chunk 262 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 295 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 233 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN ** 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** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN D1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.067645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.058072 restraints weight = 284711.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.059270 restraints weight = 158572.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.060107 restraints weight = 99865.883| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.6346 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= 0.165 Angle : 0.604 12.246 39693 Z= 0.313 Chirality : 0.045 0.225 4482 Planarity : 0.005 0.098 5138 Dihedral : 4.981 58.986 3925 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.63 % Favored : 95.17 % Rotamer: Outliers : 0.03 % Allowed : 0.75 % Favored : 99.22 % 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: -0.50 (0.14), residues: 3605 helix: 0.79 (0.19), residues: 724 sheet: -0.03 (0.17), residues: 891 loop : -0.87 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 50 HIS 0.017 0.001 HIS D1048 PHE 0.024 0.002 PHE D 275 TYR 0.022 0.002 TYR E 248 ARG 0.014 0.001 ARG E1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 1) link_NAG-ASN : angle 5.25764 ( 3) hydrogen bonds : bond 0.03858 ( 1081) hydrogen bonds : angle 6.10330 ( 3072) SS BOND : bond 0.00372 ( 42) SS BOND : angle 1.56152 ( 84) covalent geometry : bond 0.00359 (29101) covalent geometry : angle 0.59852 (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 289 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 3.056 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: 0.2562 (p90) cc_final: 0.1660 (t80) REVERT: E 304 LYS cc_start: 0.8994 (mmtm) cc_final: 0.8383 (tptp) REVERT: E 493 GLN cc_start: 0.8577 (mt0) cc_final: 0.8326 (mp10) REVERT: E 532 ASN cc_start: 0.8537 (m-40) cc_final: 0.8173 (p0) REVERT: E 562 PHE cc_start: 0.7542 (m-80) cc_final: 0.7259 (m-80) REVERT: E 740 MET cc_start: 0.7760 (tpp) cc_final: 0.7437 (tpp) REVERT: E 754 LEU cc_start: 0.8999 (mm) cc_final: 0.8713 (tt) REVERT: E 864 LEU cc_start: 0.8962 (tp) cc_final: 0.8674 (tp) REVERT: E 973 ILE cc_start: 0.7802 (mt) cc_final: 0.7531 (mt) REVERT: E 1018 ILE cc_start: 0.9380 (mm) cc_final: 0.8447 (mp) REVERT: E 1023 ASN cc_start: 0.8817 (m110) cc_final: 0.8479 (m110) REVERT: E 1030 SER cc_start: 0.8985 (m) cc_final: 0.8459 (p) REVERT: E 1031 GLU cc_start: 0.8009 (mp0) cc_final: 0.7167 (mp0) REVERT: E 1050 MET cc_start: 0.8757 (pmm) cc_final: 0.8040 (pmm) REVERT: A 177 GLN cc_start: 0.2783 (tp40) cc_final: 0.1785 (pt0) REVERT: B 145 TYR cc_start: 0.5101 (t80) cc_final: 0.4500 (t80) REVERT: C 52 GLN cc_start: 0.9201 (tt0) cc_final: 0.8133 (pm20) REVERT: C 559 PHE cc_start: 0.6254 (m-80) cc_final: 0.5857 (m-80) REVERT: C 902 MET cc_start: 0.8877 (mmm) cc_final: 0.8488 (mmp) REVERT: C 904 TYR cc_start: 0.8577 (t80) cc_final: 0.8315 (t80) REVERT: C 921 LYS cc_start: 0.9104 (mttt) cc_final: 0.8836 (pttp) REVERT: C 945 LEU cc_start: 0.7815 (tp) cc_final: 0.7613 (mp) REVERT: C 954 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8969 (tp40) REVERT: C 957 GLN cc_start: 0.8573 (tp-100) cc_final: 0.8303 (tp-100) REVERT: C 1019 ARG cc_start: 0.9013 (pmt-80) cc_final: 0.8556 (pmt-80) REVERT: D 215 ASP cc_start: 0.8114 (m-30) cc_final: 0.7887 (m-30) REVERT: D 532 ASN cc_start: 0.7814 (m-40) cc_final: 0.7310 (t0) REVERT: D 571 ASP cc_start: 0.8875 (m-30) cc_final: 0.8339 (t0) REVERT: D 697 MET cc_start: 0.7577 (mmp) cc_final: 0.7100 (mmp) REVERT: D 742 ILE cc_start: 0.8046 (mt) cc_final: 0.7717 (tp) REVERT: D 1089 PHE cc_start: 0.8173 (m-80) cc_final: 0.7948 (m-80) outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.3692 time to fit residues: 177.2786 Evaluate side-chains 208 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 3.224 ------------------------------------------------------------------------------- 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: 3.9990 chunk 153 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 180 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 273 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN ** 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 98 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.067221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.057755 restraints weight = 284136.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.058958 restraints weight = 158317.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.059761 restraints weight = 99110.535| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29144 Z= 0.171 Angle : 0.616 11.944 39693 Z= 0.322 Chirality : 0.045 0.197 4482 Planarity : 0.004 0.068 5138 Dihedral : 5.177 59.960 3925 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.60 % Favored : 95.20 % Rotamer: Outliers : 0.03 % Allowed : 0.72 % Favored : 99.25 % 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: -0.60 (0.14), residues: 3605 helix: 0.77 (0.19), residues: 719 sheet: -0.13 (0.17), residues: 886 loop : -0.94 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 50 HIS 0.017 0.002 HIS D1048 PHE 0.025 0.002 PHE D 275 TYR 0.019 0.002 TYR D 365 ARG 0.013 0.001 ARG E1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00012 ( 1) link_NAG-ASN : angle 5.17940 ( 3) hydrogen bonds : bond 0.03912 ( 1081) hydrogen bonds : angle 6.17711 ( 3072) SS BOND : bond 0.00443 ( 42) SS BOND : angle 1.40742 ( 84) covalent geometry : bond 0.00373 (29101) covalent geometry : angle 0.61192 (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 275 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 3.541 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: E 175 PHE cc_start: 0.2249 (p90) cc_final: 0.1393 (t80) REVERT: E 304 LYS cc_start: 0.8998 (mmtm) cc_final: 0.8396 (tptp) REVERT: E 360 ASN cc_start: 0.6507 (t0) cc_final: 0.6243 (t0) REVERT: E 493 GLN cc_start: 0.8475 (mt0) cc_final: 0.8127 (mp10) REVERT: E 532 ASN cc_start: 0.8504 (m-40) cc_final: 0.8179 (p0) REVERT: E 754 LEU cc_start: 0.8966 (mm) cc_final: 0.8703 (tt) REVERT: E 973 ILE cc_start: 0.7889 (mt) cc_final: 0.7604 (mt) REVERT: E 993 ILE cc_start: 0.9014 (mt) cc_final: 0.8736 (mt) REVERT: E 997 ILE cc_start: 0.9585 (pt) cc_final: 0.9305 (tt) REVERT: E 1018 ILE cc_start: 0.9073 (mm) cc_final: 0.8809 (mm) REVERT: E 1023 ASN cc_start: 0.8791 (m110) cc_final: 0.8475 (m110) REVERT: E 1029 MET cc_start: 0.8564 (mmp) cc_final: 0.8357 (mmm) REVERT: E 1030 SER cc_start: 0.8889 (m) cc_final: 0.8257 (p) REVERT: E 1033 VAL cc_start: 0.8764 (t) cc_final: 0.8536 (t) REVERT: E 1050 MET cc_start: 0.8543 (pmm) cc_final: 0.7937 (pmm) REVERT: A 177 GLN cc_start: 0.3121 (tp40) cc_final: 0.2017 (pt0) REVERT: B 168 TRP cc_start: 0.4938 (t60) cc_final: 0.4564 (t60) REVERT: C 559 PHE cc_start: 0.6095 (m-80) cc_final: 0.5662 (m-80) REVERT: C 921 LYS cc_start: 0.9081 (mttt) cc_final: 0.8862 (pttp) REVERT: C 957 GLN cc_start: 0.8454 (tp-100) cc_final: 0.8249 (tp-100) REVERT: C 1019 ARG cc_start: 0.8836 (pmt-80) cc_final: 0.8351 (pmt-80) REVERT: D 153 MET cc_start: 0.6250 (pmm) cc_final: 0.6046 (pmm) REVERT: D 177 MET cc_start: 0.3621 (mtm) cc_final: 0.2346 (mmt) REVERT: D 532 ASN cc_start: 0.7652 (m-40) cc_final: 0.7231 (t0) REVERT: D 571 ASP cc_start: 0.8727 (m-30) cc_final: 0.8258 (t0) REVERT: D 742 ILE cc_start: 0.7993 (mt) cc_final: 0.7652 (tp) REVERT: D 994 ASP cc_start: 0.7904 (t0) cc_final: 0.7556 (t0) REVERT: D 1118 ASP cc_start: 0.8043 (p0) cc_final: 0.7729 (t70) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.3774 time to fit residues: 174.2027 Evaluate side-chains 205 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 3.274 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 0.0470 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 0.0770 chunk 190 optimal weight: 10.0000 chunk 339 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 321 optimal weight: 0.0170 chunk 244 optimal weight: 9.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN E 149 ASN E 370 ASN ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 170 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 954 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.069019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.059574 restraints weight = 280261.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.060797 restraints weight = 155915.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.061575 restraints weight = 98030.018| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.6521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29144 Z= 0.117 Angle : 0.577 11.912 39693 Z= 0.298 Chirality : 0.045 0.179 4482 Planarity : 0.004 0.064 5138 Dihedral : 4.720 54.104 3925 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.11 % Favored : 95.70 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % 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: -0.47 (0.14), residues: 3605 helix: 0.78 (0.19), residues: 718 sheet: -0.01 (0.17), residues: 877 loop : -0.83 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 50 HIS 0.015 0.001 HIS D1048 PHE 0.019 0.002 PHE D 275 TYR 0.019 0.002 TYR E1110 ARG 0.008 0.000 ARG E1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 1) link_NAG-ASN : angle 3.99742 ( 3) hydrogen bonds : bond 0.03660 ( 1081) hydrogen bonds : angle 5.89466 ( 3072) SS BOND : bond 0.00321 ( 42) SS BOND : angle 1.30409 ( 84) covalent geometry : bond 0.00261 (29101) covalent geometry : angle 0.57304 (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 311 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 3.575 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: E 153 MET cc_start: 0.6443 (mmm) cc_final: 0.6146 (mtp) REVERT: E 175 PHE cc_start: 0.1753 (p90) cc_final: 0.1154 (t80) REVERT: E 304 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8366 (tptp) REVERT: E 448 ASN cc_start: 0.6682 (t0) cc_final: 0.5480 (m110) REVERT: E 493 GLN cc_start: 0.8430 (mt0) cc_final: 0.8124 (mp10) REVERT: E 532 ASN cc_start: 0.8393 (m-40) cc_final: 0.8109 (p0) REVERT: E 740 MET cc_start: 0.7728 (tpp) cc_final: 0.7487 (tpp) REVERT: E 752 LEU cc_start: 0.8772 (mm) cc_final: 0.8311 (mm) REVERT: E 754 LEU cc_start: 0.8944 (mm) cc_final: 0.8584 (tt) REVERT: E 864 LEU cc_start: 0.8704 (tp) cc_final: 0.8227 (tt) REVERT: E 873 TYR cc_start: 0.8651 (m-80) cc_final: 0.8199 (m-80) REVERT: E 973 ILE cc_start: 0.7730 (mt) cc_final: 0.7491 (mt) REVERT: E 1017 GLU cc_start: 0.7994 (pp20) cc_final: 0.7650 (pp20) REVERT: E 1023 ASN cc_start: 0.8747 (m110) cc_final: 0.8462 (m110) REVERT: E 1030 SER cc_start: 0.8892 (m) cc_final: 0.8040 (p) REVERT: E 1031 GLU cc_start: 0.7848 (mp0) cc_final: 0.6919 (mp0) REVERT: E 1050 MET cc_start: 0.8426 (pmm) cc_final: 0.8037 (pmm) REVERT: A 78 THR cc_start: 0.7070 (m) cc_final: 0.6833 (m) REVERT: A 177 GLN cc_start: 0.2835 (tp40) cc_final: 0.1702 (pt0) REVERT: C 52 GLN cc_start: 0.9090 (tt0) cc_final: 0.8099 (pm20) REVERT: C 559 PHE cc_start: 0.6017 (m-80) cc_final: 0.5623 (m-80) REVERT: C 904 TYR cc_start: 0.8491 (t80) cc_final: 0.8179 (t80) REVERT: C 921 LYS cc_start: 0.9088 (mttt) cc_final: 0.8834 (pttp) REVERT: C 957 GLN cc_start: 0.8315 (tp-100) cc_final: 0.8094 (tp-100) REVERT: C 1019 ARG cc_start: 0.8757 (pmt-80) cc_final: 0.8379 (pmt-80) REVERT: C 1031 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8210 (mm-30) REVERT: D 153 MET cc_start: 0.6169 (pmm) cc_final: 0.5948 (pmm) REVERT: D 177 MET cc_start: 0.3340 (mtm) cc_final: 0.1920 (mmt) REVERT: D 532 ASN cc_start: 0.7548 (m-40) cc_final: 0.7121 (t0) REVERT: D 571 ASP cc_start: 0.8548 (m-30) cc_final: 0.8121 (t0) REVERT: D 697 MET cc_start: 0.7215 (mmp) cc_final: 0.6990 (mmp) REVERT: D 773 GLU cc_start: 0.8549 (tt0) cc_final: 0.8335 (tt0) REVERT: D 954 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7992 (tm-30) REVERT: D 994 ASP cc_start: 0.7808 (t0) cc_final: 0.7497 (t0) REVERT: D 1031 GLU cc_start: 0.7656 (mp0) cc_final: 0.7123 (mt-10) REVERT: D 1089 PHE cc_start: 0.7980 (m-80) cc_final: 0.7650 (m-80) REVERT: D 1118 ASP cc_start: 0.7969 (p0) cc_final: 0.7659 (t70) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.3685 time to fit residues: 192.5866 Evaluate side-chains 219 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 3.164 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 314 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 313 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN E 149 ASN E 245 HIS ** 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** C 99 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 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** D 751 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.065055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.055734 restraints weight = 286522.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.057101 restraints weight = 165732.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.057964 restraints weight = 96793.457| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.7335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29144 Z= 0.293 Angle : 0.769 11.830 39693 Z= 0.405 Chirality : 0.049 0.215 4482 Planarity : 0.006 0.063 5138 Dihedral : 5.665 58.774 3925 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.88 % Favored : 93.93 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % 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: -0.92 (0.13), residues: 3605 helix: 0.44 (0.19), residues: 729 sheet: -0.32 (0.17), residues: 853 loop : -1.14 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 50 HIS 0.015 0.002 HIS D1048 PHE 0.032 0.003 PHE E 392 TYR 0.028 0.003 TYR E 453 ARG 0.017 0.001 ARG E1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 5.89058 ( 3) hydrogen bonds : bond 0.04604 ( 1081) hydrogen bonds : angle 6.57323 ( 3072) SS BOND : bond 0.00596 ( 42) SS BOND : angle 1.51250 ( 84) covalent geometry : bond 0.00629 (29101) covalent geometry : angle 0.76504 (39606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9718.26 seconds wall clock time: 169 minutes 46.12 seconds (10186.12 seconds total)