Starting phenix.real_space_refine on Tue Oct 27 11:22:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7byr_30247/10_2026/7byr_30247.cif Found real_map, /net/cci-nas-00/data/ceres_data/7byr_30247/10_2026/7byr_30247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7byr_30247/10_2026/7byr_30247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7byr_30247/10_2026/7byr_30247.map" model { file = "/net/cci-nas-00/data/ceres_data/7byr_30247/10_2026/7byr_30247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7byr_30247/10_2026/7byr_30247.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7byr_30247/10_2026/7byr_30247.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7byr_30247/10_2026/7byr_30247.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 110 5.16 5 C 15644 2.51 5 N 4012 2.21 5 O 4796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 223 residue(s): 0.08s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24562 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7311 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 46, 'TRANS': 912} Chain breaks: 13 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 5, 'ASP:plan': 8, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 7681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7681 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 49, 'TRANS': 948} Chain breaks: 9 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 7327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7327 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 13 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 10, 'GLN:plan1': 6, 'PHE:plan': 5, 'TYR:plan': 4, 'ASP:plan': 11, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 209 Chain: "H" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 807 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.70, per 1000 atoms: 0.23 Number of scatterers: 24562 At special positions: 0 Unit cell: (136.095, 136.095, 198.34, 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 110 16.00 O 4796 8.00 N 4012 7.00 C 15644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.01 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN A 282 " " NAG A1314 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 282 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B1074 " " NAG B1314 " - " ASN B 343 " " NAG C1301 " - " ASN C1134 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 801 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 616 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 234 " " NAG C1313 " - " ASN C 282 " " NAG C1314 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN C1098 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 165 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 848.2 milliseconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5884 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 48 sheets defined 24.1% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.571A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.017A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.838A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.132A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 4.247A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.546A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.846A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.637A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.117A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.746A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.961A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.788A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.576A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.931A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.379A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.795A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.565A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1120 removed outlier: 3.994A pdb=" N THR B1120 " --> pdb=" O THR B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.901A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.623A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.982A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 738 through 744 removed outlier: 3.662A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.611A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.924A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.545A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.715A 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 981 removed outlier: 3.541A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.727A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.658A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.822A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.683A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.864A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.974A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 327 removed outlier: 7.535A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.116A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.910A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.012A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.571A pdb=" N ILE B 788 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.554A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.031A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.847A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 103 through 104 removed outlier: 3.951A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.544A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.636A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 removed outlier: 4.056A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.071A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 3.732A pdb=" N ILE C 788 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.488A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.344A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 5.230A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.881A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.840A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.116A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.838A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.647A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE C 515 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N CYS C 432 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS C 378 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE C 434 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR C 376 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.587A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.898A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.372A 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 1125 removed outlier: 5.007A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1096 removed outlier: 4.917A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.648A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 46 through 47 Processing sheet with id=AE9, first strand: chain 'H' and resid 46 through 47 Processing sheet with id=AF1, first strand: chain 'H' and resid 68 through 69 Processing sheet with id=AF2, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.841A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2583 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: 5.06 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7809 1.35 - 1.48: 6689 1.48 - 1.61: 10446 1.61 - 1.74: 1 1.74 - 1.88: 137 Bond restraints: 25082 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N MET H 34 " pdb=" CA MET H 34 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.29e-02 6.01e+03 6.17e+00 bond pdb=" N ALA H 33 " pdb=" CA ALA H 33 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.09e-02 8.42e+03 6.07e+00 bond pdb=" N SER H 31 " pdb=" CA SER H 31 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.62e+00 bond pdb=" N TYR H 32 " pdb=" CA TYR H 32 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.36e-02 5.41e+03 5.40e+00 ... (remaining 25077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 33885 3.49 - 6.99: 261 6.99 - 10.48: 20 10.48 - 13.97: 6 13.97 - 17.47: 1 Bond angle restraints: 34173 Sorted by residual: angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 131.87 -17.47 2.30e+00 1.89e-01 5.77e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 125.96 -11.56 2.30e+00 1.89e-01 2.53e+01 angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 125.01 -10.61 2.30e+00 1.89e-01 2.13e+01 angle pdb=" N ASN B 542 " pdb=" CA ASN B 542 " pdb=" C ASN B 542 " ideal model delta sigma weight residual 110.80 101.18 9.62 2.13e+00 2.20e-01 2.04e+01 angle pdb=" C SER C1030 " pdb=" N GLU C1031 " pdb=" CA GLU C1031 " ideal model delta sigma weight residual 122.65 115.81 6.84 1.60e+00 3.91e-01 1.83e+01 ... (remaining 34168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12706 17.99 - 35.97: 1391 35.97 - 53.96: 325 53.96 - 71.94: 51 71.94 - 89.93: 30 Dihedral angle restraints: 14503 sinusoidal: 5390 harmonic: 9113 Sorted by residual: 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 3.50 89.50 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 5.64 87.36 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 13.22 79.78 1 1.00e+01 1.00e-02 7.90e+01 ... (remaining 14500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3419 0.073 - 0.145: 619 0.145 - 0.218: 37 0.218 - 0.290: 7 0.290 - 0.363: 4 Chirality restraints: 4086 Sorted by residual: chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 4083 not shown) Planarity restraints: 4383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.039 2.00e-02 2.50e+03 3.70e-02 1.71e+01 pdb=" CG ASN B 616 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " 0.041 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " -0.025 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP B 886 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 105 " -0.023 2.00e-02 2.50e+03 1.84e-02 8.50e+00 pdb=" CG TRP H 105 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP H 105 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP H 105 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 105 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 105 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 105 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 105 " -0.004 2.00e-02 2.50e+03 ... (remaining 4380 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 18 2.20 - 2.88: 10138 2.88 - 3.55: 34047 3.55 - 4.23: 53005 4.23 - 4.90: 91511 Nonbonded interactions: 188719 Sorted by model distance: nonbonded pdb=" O GLN H 3 " pdb=" C SER H 25 " model vdw 1.529 3.270 nonbonded pdb=" N GLN H 3 " pdb=" O SER H 25 " model vdw 1.877 3.120 nonbonded pdb=" O CYS C1032 " pdb=" OG SER C1051 " model vdw 2.004 3.040 nonbonded pdb=" O CYS B1032 " pdb=" OG SER B1051 " model vdw 2.061 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.083 3.040 ... (remaining 188714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 66 or resid 81 through 95 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 104 or (resid 105 and (name N or name CA or name C or name O \ or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA or n \ ame C or name O or name CB )) or resid 130 through 140 or (resid 157 through 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 1 \ 87 or (resid 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 through 194 or (resid 195 through 198 and (name N or name CA or name C or \ name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 209 or resid 217 through 236 or ( \ resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ or (resid 239 and (name N or name CA or name C or name O or name CB )) or resid \ 240 through 243 or resid 264 through 350 or (resid 351 through 352 and (name N o \ r name CA or name C or name O or name CB )) or resid 353 through 363 or (resid 3 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 365 through \ 368 or (resid 369 and (name N or name CA or name C or name O or name CB )) or r \ esid 370 through 373 or (resid 374 and (name N or name CA or name C or name O or \ name CB )) or resid 375 through 407 or (resid 408 and (name N or name CA or nam \ e C or name O or name CB )) or resid 409 through 441 or (resid 442 and (name N o \ r name CA or name C or name O or name CB )) or resid 443 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 496 or (res \ id 497 through 498 and (name N or name CA or name C or name O or name CB )) or r \ esid 503 through 508 or (resid 509 and (name N or name CA or name C or name O or \ name CB )) or resid 510 through 620 or resid 641 through 1312)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 or (resid 239 and (n \ ame N or name CA or name C or name O or name CB )) or resid 240 through 289 or ( \ resid 290 and (name N or name CA or name C or name O or name CB )) or resid 291 \ through 328 or (resid 335 and (name N or name CA or name C or name O or name CB \ )) or resid 336 through 339 or (resid 340 and (name N or name CA or name C or na \ me O or name CB )) or resid 341 through 345 or (resid 346 and (name N or name CA \ or name C or name O or name CB )) or resid 347 through 348 or (resid 349 and (n \ ame N or name CA or name C or name O or name CB )) or resid 350 or (resid 351 th \ rough 352 and (name N or name CA or name C or name O or name CB )) or resid 353 \ through 363 or (resid 364 and (name N or name CA or name C or name O or name CB \ )) or resid 365 through 368 or (resid 369 and (name N or name CA or name C or na \ me O or name CB )) or resid 370 through 373 or (resid 374 and (name N or name CA \ or name C or name O or name CB )) or resid 375 through 397 or (resid 398 and (n \ ame N or name CA or name C or name O or name CB )) or resid 399 through 402 or ( \ resid 403 and (name N or name CA or name C or name O or name CB )) or resid 404 \ or (resid 405 through 408 and (name N or name CA or name C or name O or name CB \ )) or resid 409 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or resid 416 or (resid 417 and (name N or name CA \ or name C or name O or name CB )) or resid 418 through 419 or (resid 420 and (n \ ame N or name CA or name C or name O or name CB )) or resid 421 through 423 or ( \ resid 424 and (name N or name CA or name C or name O or name CB )) or resid 425 \ through 426 or (resid 427 through 428 and (name N or name CA or name C or name O \ or name CB )) or resid 429 through 440 or (resid 441 through 442 and (name N or \ name CA or name C or name O or name CB )) or resid 443 or (resid 449 and (name \ N or name CA or name C or name O or name CB )) or resid 450 through 453 or (resi \ d 454 and (name N or name CA or name C or name O or name CB )) or resid 491 or ( \ resid 492 through 493 and (name N or name CA or name C or name O or name CB )) o \ r resid 494 through 496 or (resid 497 through 498 and (name N or name CA or name \ C or name O or name CB )) or resid 503 through 508 or (resid 509 and (name N or \ name CA or name C or name O or name CB )) or resid 510 through 515 or (resid 51 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 517 through \ 518 or (resid 519 through 520 and (name N or name CA or name C or name O or name \ CB )) or resid 521 through 527 or (resid 528 through 529 and (name N or name CA \ or name C or name O or name CB )) or resid 530 through 620 or resid 641 through \ 1314)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 66 or resid 81 throug \ h 95 or (resid 99 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 104 or (resid 105 and (name N or name CA or name C o \ r name O or name CB )) or resid 106 through 187 or (resid 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 199 or (resid 200 an \ d (name N or name CA or name C or name O or name CB )) or resid 201 through 209 \ or resid 217 through 243 or resid 264 through 328 or resid 335 through 454 or re \ sid 491 through 1314)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' } 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: 5.830 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: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 22.580 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.006 0.082 25165 Z= 0.283 Angle : 0.968 17.466 34384 Z= 0.510 Chirality : 0.054 0.363 4086 Planarity : 0.005 0.054 4345 Dihedral : 15.984 89.927 8505 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.27 % Allowed : 1.39 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3051 helix: 0.47 (0.21), residues: 629 sheet: -1.01 (0.19), residues: 675 loop : -2.24 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 466 TYR 0.041 0.003 TYR B1067 PHE 0.031 0.003 PHE A 168 TRP 0.055 0.004 TRP B 886 HIS 0.011 0.002 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.28 (25082) covalent geometry : angle 0.91794 / 0.50 (34173) SS BOND : bond 0.00836 / 0.51 ( 38) SS BOND : angle 3.75261 / 2.47 ( 76) hydrogen bonds : bond 0.14192 / 9.65 ( 957) hydrogen bonds : angle 7.26192 / 5.06 ( 2583) link_BETA1-4 : bond 0.00743 / 0.56 ( 7) link_BETA1-4 : angle 2.56557 / 1.49 ( 21) link_NAG-ASN : bond 0.00609 / 0.42 ( 38) link_NAG-ASN : angle 4.38937 / 3.01 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6465 (t80) cc_final: 0.6091 (t80) REVERT: A 170 TYR cc_start: 0.6729 (m-80) cc_final: 0.6453 (m-80) REVERT: A 229 LEU cc_start: 0.7192 (mm) cc_final: 0.6951 (tp) REVERT: A 238 PHE cc_start: 0.6235 (p90) cc_final: 0.5806 (p90) REVERT: A 740 MET cc_start: 0.7051 (tmm) cc_final: 0.6409 (tpp) REVERT: H 50 TRP cc_start: 0.8045 (t60) cc_final: 0.7841 (t60) REVERT: L 24 ARG cc_start: 0.7281 (mtp180) cc_final: 0.6779 (mtm-85) outliers start: 7 outliers final: 2 residues processed: 205 average time/residue: 0.1479 time to fit residues: 50.4215 Evaluate side-chains 166 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain L residue 92 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 239 GLN A 388 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 907 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 474 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 787 GLN B 824 ASN B 949 GLN B 953 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 949 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.100776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.078351 restraints weight = 69430.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078655 restraints weight = 43171.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079282 restraints weight = 32812.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080020 restraints weight = 29851.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080018 restraints weight = 26536.194| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25165 Z= 0.163 Angle : 0.758 12.834 34384 Z= 0.375 Chirality : 0.048 0.275 4086 Planarity : 0.005 0.050 4345 Dihedral : 5.459 32.507 3320 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.51 % Allowed : 12.12 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.15), residues: 3051 helix: 1.03 (0.21), residues: 614 sheet: -0.85 (0.19), residues: 674 loop : -2.13 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 815 TYR 0.032 0.002 TYR B 904 PHE 0.020 0.002 PHE B 342 TRP 0.033 0.002 TRP H 105 HIS 0.008 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (25082) covalent geometry : angle 0.72021 / 0.37 (34173) SS BOND : bond 0.00623 / 0.39 ( 38) SS BOND : angle 2.63433 / 1.70 ( 76) hydrogen bonds : bond 0.04855 / 3.29 ( 957) hydrogen bonds : angle 6.08739 / 4.20 ( 2583) link_BETA1-4 : bond 0.01022 / 0.69 ( 7) link_BETA1-4 : angle 2.29297 / 1.34 ( 21) link_NAG-ASN : bond 0.00458 / 0.30 ( 38) link_NAG-ASN : angle 3.47015 / 2.36 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8866 (mm) cc_final: 0.8474 (pp) REVERT: A 92 PHE cc_start: 0.6471 (t80) cc_final: 0.6203 (t80) REVERT: A 238 PHE cc_start: 0.5965 (p90) cc_final: 0.5709 (p90) REVERT: A 740 MET cc_start: 0.7583 (tmm) cc_final: 0.6851 (tpp) REVERT: C 904 TYR cc_start: 0.7214 (t80) cc_final: 0.6901 (t80) REVERT: H 6 GLN cc_start: 0.6510 (OUTLIER) cc_final: 0.5825 (mt0) REVERT: H 50 TRP cc_start: 0.7954 (t60) cc_final: 0.7610 (t60) REVERT: H 100 GLN cc_start: 0.6039 (mt0) cc_final: 0.5649 (mp10) REVERT: H 104 SER cc_start: 0.9015 (t) cc_final: 0.8792 (p) outliers start: 39 outliers final: 21 residues processed: 210 average time/residue: 0.1399 time to fit residues: 50.0649 Evaluate side-chains 183 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [205, 13, 118, 261, 41, 294, 177, 206, 64, 163, 208] chunk 205 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 294 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 chunk 206 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 163 optimal weight: 0.0470 chunk 208 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN A 563 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 394 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 762 GLN C 954 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.100786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078212 restraints weight = 69372.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078695 restraints weight = 43308.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.079385 restraints weight = 32386.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.079726 restraints weight = 27501.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079788 restraints weight = 24674.322| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25165 Z= 0.133 Angle : 0.684 12.656 34384 Z= 0.337 Chirality : 0.046 0.330 4086 Planarity : 0.004 0.063 4345 Dihedral : 5.074 32.641 3318 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.89 % Allowed : 15.13 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 3051 helix: 1.34 (0.21), residues: 611 sheet: -0.68 (0.19), residues: 660 loop : -1.92 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 319 TYR 0.021 0.001 TYR H 111 PHE 0.018 0.001 PHE A 377 TRP 0.021 0.002 TRP H 105 HIS 0.007 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (25082) covalent geometry : angle 0.64979 / 0.33 (34173) SS BOND : bond 0.00539 / 0.36 ( 38) SS BOND : angle 2.51126 / 1.65 ( 76) hydrogen bonds : bond 0.04350 / 2.96 ( 957) hydrogen bonds : angle 5.69925 / 3.92 ( 2583) link_BETA1-4 : bond 0.00859 / 0.66 ( 7) link_BETA1-4 : angle 2.13693 / 1.25 ( 21) link_NAG-ASN : bond 0.00437 / 0.26 ( 38) link_NAG-ASN : angle 3.10077 / 2.07 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6370 (t80) cc_final: 0.6104 (t80) REVERT: A 740 MET cc_start: 0.7668 (tmm) cc_final: 0.6938 (tpp) REVERT: B 346 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7815 (tpp80) REVERT: B 873 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.8427 (m-10) REVERT: C 51 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8774 (p) REVERT: C 904 TYR cc_start: 0.7117 (t80) cc_final: 0.6477 (t80) REVERT: H 50 TRP cc_start: 0.7895 (t60) cc_final: 0.7484 (t60) REVERT: H 105 TRP cc_start: 0.8191 (OUTLIER) cc_final: 0.7492 (p-90) outliers start: 49 outliers final: 32 residues processed: 217 average time/residue: 0.1325 time to fit residues: 49.2680 Evaluate side-chains 192 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [259, 182, 151, 85, 307, 164, 213, 114, 215, 202, 282] chunk 259 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 307 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 282 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.100844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077950 restraints weight = 68890.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078857 restraints weight = 41518.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079622 restraints weight = 29597.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079812 restraints weight = 25785.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079896 restraints weight = 23117.488| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25165 Z= 0.133 Angle : 0.649 12.491 34384 Z= 0.318 Chirality : 0.046 0.306 4086 Planarity : 0.004 0.071 4345 Dihedral : 4.787 30.022 3316 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.70 % Allowed : 16.52 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.15), residues: 3051 helix: 1.46 (0.21), residues: 612 sheet: -0.65 (0.19), residues: 668 loop : -1.77 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.022 0.001 TYR C 904 PHE 0.014 0.001 PHE A 377 TRP 0.019 0.001 TRP H 105 HIS 0.006 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (25082) covalent geometry : angle 0.61901 / 0.31 (34173) SS BOND : bond 0.00484 / 0.33 ( 38) SS BOND : angle 2.26378 / 1.50 ( 76) hydrogen bonds : bond 0.04125 / 2.81 ( 957) hydrogen bonds : angle 5.47389 / 3.75 ( 2583) link_BETA1-4 : bond 0.00881 / 0.63 ( 7) link_BETA1-4 : angle 2.07050 / 1.21 ( 21) link_NAG-ASN : bond 0.00394 / 0.23 ( 38) link_NAG-ASN : angle 2.80632 / 1.87 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 172 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6524 (t80) cc_final: 0.6237 (t80) REVERT: A 229 LEU cc_start: 0.6989 (mm) cc_final: 0.6744 (tp) REVERT: A 740 MET cc_start: 0.7653 (tmm) cc_final: 0.6908 (tpp) REVERT: B 324 GLU cc_start: 0.7748 (tp30) cc_final: 0.7399 (tp30) REVERT: B 515 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: B 873 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8456 (m-10) REVERT: C 51 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8806 (p) REVERT: C 904 TYR cc_start: 0.7070 (t80) cc_final: 0.6833 (t80) REVERT: H 50 TRP cc_start: 0.7890 (t60) cc_final: 0.7448 (t60) REVERT: H 105 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.7605 (p-90) REVERT: H 111 TYR cc_start: 0.5947 (OUTLIER) cc_final: 0.5702 (t80) REVERT: H 113 MET cc_start: 0.4931 (mpp) cc_final: 0.4660 (mpp) outliers start: 70 outliers final: 47 residues processed: 225 average time/residue: 0.1376 time to fit residues: 52.9242 Evaluate side-chains 205 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 111 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [106, 143, 82, 249, 220, 251, 269, 93, 212, 2, 298] chunk 106 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 251 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 93 optimal weight: 0.0970 chunk 212 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C1048 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078064 restraints weight = 69140.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.078736 restraints weight = 41976.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.079369 restraints weight = 30724.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079642 restraints weight = 26930.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079740 restraints weight = 24899.269| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25165 Z= 0.130 Angle : 0.632 12.304 34384 Z= 0.310 Chirality : 0.045 0.311 4086 Planarity : 0.004 0.073 4345 Dihedral : 4.648 29.829 3316 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.13 % Allowed : 17.33 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 3051 helix: 1.54 (0.21), residues: 618 sheet: -0.60 (0.19), residues: 667 loop : -1.70 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.020 0.001 TYR C 904 PHE 0.014 0.001 PHE A 377 TRP 0.017 0.001 TRP H 105 HIS 0.006 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (25082) covalent geometry : angle 0.60512 / 0.30 (34173) SS BOND : bond 0.00584 / 0.40 ( 38) SS BOND : angle 2.09514 / 1.43 ( 76) hydrogen bonds : bond 0.04028 / 2.75 ( 957) hydrogen bonds : angle 5.37327 / 3.68 ( 2583) link_BETA1-4 : bond 0.00860 / 0.62 ( 7) link_BETA1-4 : angle 2.05468 / 1.20 ( 21) link_NAG-ASN : bond 0.00404 / 0.22 ( 38) link_NAG-ASN : angle 2.62790 / 1.73 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 165 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6485 (t80) cc_final: 0.6217 (t80) REVERT: A 229 LEU cc_start: 0.7045 (mm) cc_final: 0.6810 (tp) REVERT: A 324 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7172 (pp20) REVERT: A 740 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7018 (tpp) REVERT: A 990 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8526 (tm-30) REVERT: B 324 GLU cc_start: 0.7743 (tp30) cc_final: 0.7352 (tp30) REVERT: B 515 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: B 873 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8397 (m-10) REVERT: C 51 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8819 (p) REVERT: H 50 TRP cc_start: 0.7894 (t60) cc_final: 0.7596 (t60) REVERT: H 62 GLN cc_start: 0.8371 (pp30) cc_final: 0.8120 (pp30) REVERT: H 105 TRP cc_start: 0.8231 (OUTLIER) cc_final: 0.7662 (p-90) REVERT: H 111 TYR cc_start: 0.6097 (OUTLIER) cc_final: 0.5863 (t80) REVERT: H 113 MET cc_start: 0.5265 (mpp) cc_final: 0.4883 (mpp) REVERT: L 49 TYR cc_start: 0.8141 (p90) cc_final: 0.7714 (p90) outliers start: 81 outliers final: 53 residues processed: 225 average time/residue: 0.1359 time to fit residues: 52.4822 Evaluate side-chains 214 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 111 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [222, 49, 168, 6, 268, 300, 91, 310, 35, 303, 46] chunk 222 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 300 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 310 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.098410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.075737 restraints weight = 69616.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.075913 restraints weight = 47912.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.076344 restraints weight = 39848.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.076681 restraints weight = 33811.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.076874 restraints weight = 29236.757| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25165 Z= 0.209 Angle : 0.687 12.179 34384 Z= 0.338 Chirality : 0.047 0.303 4086 Planarity : 0.004 0.078 4345 Dihedral : 4.827 29.463 3316 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.90 % Allowed : 18.49 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 3051 helix: 1.36 (0.21), residues: 626 sheet: -0.70 (0.19), residues: 681 loop : -1.72 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 319 TYR 0.022 0.002 TYR C1067 PHE 0.020 0.002 PHE A 970 TRP 0.040 0.002 TRP C 886 HIS 0.006 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (25082) covalent geometry : angle 0.66014 / 0.33 (34173) SS BOND : bond 0.00579 / 0.39 ( 38) SS BOND : angle 2.39583 / 1.58 ( 76) hydrogen bonds : bond 0.04486 / 3.09 ( 957) hydrogen bonds : angle 5.49756 / 3.78 ( 2583) link_BETA1-4 : bond 0.00868 / 0.61 ( 7) link_BETA1-4 : angle 2.11645 / 1.22 ( 21) link_NAG-ASN : bond 0.00500 / 0.30 ( 38) link_NAG-ASN : angle 2.67998 / 1.75 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 164 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6580 (t80) cc_final: 0.6228 (t80) REVERT: A 229 LEU cc_start: 0.7098 (mm) cc_final: 0.6849 (tp) REVERT: A 324 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7164 (pp20) REVERT: A 740 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7290 (tpp) REVERT: A 990 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8605 (tm-30) REVERT: B 515 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: B 873 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8514 (m-10) REVERT: B 977 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8072 (mp) REVERT: C 34 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7250 (mmp80) REVERT: C 51 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8865 (p) REVERT: H 6 GLN cc_start: 0.6605 (OUTLIER) cc_final: 0.6390 (mt0) REVERT: H 105 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.7840 (p-90) REVERT: H 111 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.6294 (t80) REVERT: H 113 MET cc_start: 0.5924 (mpp) cc_final: 0.5588 (mpp) REVERT: L 49 TYR cc_start: 0.8236 (p90) cc_final: 0.7862 (p90) outliers start: 101 outliers final: 72 residues processed: 244 average time/residue: 0.1304 time to fit residues: 54.3451 Evaluate side-chains 234 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 152 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [249, 270, 216, 23, 37, 66, 285, 117, 194, 191, 8] chunk 249 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 0.0770 chunk 66 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.099874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.077184 restraints weight = 68810.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077668 restraints weight = 42520.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.078113 restraints weight = 31864.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.078389 restraints weight = 29028.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.078513 restraints weight = 26354.049| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25165 Z= 0.138 Angle : 0.642 12.049 34384 Z= 0.315 Chirality : 0.046 0.320 4086 Planarity : 0.004 0.074 4345 Dihedral : 4.677 28.979 3316 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.47 % Allowed : 20.11 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 3051 helix: 1.49 (0.21), residues: 627 sheet: -0.65 (0.19), residues: 670 loop : -1.64 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.018 0.001 TYR C1067 PHE 0.015 0.001 PHE A 238 TRP 0.042 0.002 TRP C 886 HIS 0.007 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (25082) covalent geometry : angle 0.61773 / 0.31 (34173) SS BOND : bond 0.00598 / 0.42 ( 38) SS BOND : angle 2.16737 / 1.45 ( 76) hydrogen bonds : bond 0.04143 / 2.84 ( 957) hydrogen bonds : angle 5.33562 / 3.67 ( 2583) link_BETA1-4 : bond 0.00830 / 0.60 ( 7) link_BETA1-4 : angle 2.04528 / 1.20 ( 21) link_NAG-ASN : bond 0.00391 / 0.22 ( 38) link_NAG-ASN : angle 2.48112 / 1.61 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 164 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6534 (t80) cc_final: 0.6250 (t80) REVERT: A 229 LEU cc_start: 0.7208 (mm) cc_final: 0.6900 (tp) REVERT: A 324 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7093 (pp20) REVERT: A 740 MET cc_start: 0.7934 (tmm) cc_final: 0.7258 (tpp) REVERT: B 515 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: B 543 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7377 (t80) REVERT: B 873 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: C 34 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7152 (mmp80) REVERT: C 51 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8833 (p) REVERT: H 105 TRP cc_start: 0.8357 (OUTLIER) cc_final: 0.7768 (p-90) REVERT: H 111 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.6150 (t80) REVERT: L 49 TYR cc_start: 0.8202 (p90) cc_final: 0.7848 (p90) outliers start: 90 outliers final: 70 residues processed: 240 average time/residue: 0.1318 time to fit residues: 54.6287 Evaluate side-chains 231 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 153 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [131, 67, 206, 97, 79, 86, 203, 285, 13, 50, 307] chunk 131 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 50 optimal weight: 0.2980 chunk 307 optimal weight: 0.2980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076692 restraints weight = 69117.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077305 restraints weight = 43142.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077749 restraints weight = 32294.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.078030 restraints weight = 28640.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078173 restraints weight = 26130.475| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25165 Z= 0.159 Angle : 0.653 11.913 34384 Z= 0.319 Chirality : 0.046 0.289 4086 Planarity : 0.004 0.074 4345 Dihedral : 4.666 28.632 3316 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.63 % Allowed : 20.53 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.15), residues: 3051 helix: 1.46 (0.21), residues: 633 sheet: -0.64 (0.19), residues: 675 loop : -1.65 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.021 0.001 TYR C 904 PHE 0.015 0.001 PHE A 970 TRP 0.043 0.002 TRP C 886 HIS 0.006 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (25082) covalent geometry : angle 0.62725 / 0.31 (34173) SS BOND : bond 0.00559 / 0.39 ( 38) SS BOND : angle 2.10906 / 1.42 ( 76) hydrogen bonds : bond 0.04159 / 2.86 ( 957) hydrogen bonds : angle 5.32228 / 3.66 ( 2583) link_BETA1-4 : bond 0.00869 / 0.61 ( 7) link_BETA1-4 : angle 2.02518 / 1.18 ( 21) link_NAG-ASN : bond 0.00417 / 0.24 ( 38) link_NAG-ASN : angle 2.61680 / 1.69 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 156 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6471 (t80) cc_final: 0.6165 (t80) REVERT: A 203 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7915 (mt) REVERT: A 229 LEU cc_start: 0.7141 (mm) cc_final: 0.6817 (tp) REVERT: A 324 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7100 (pp20) REVERT: A 739 THR cc_start: 0.7898 (m) cc_final: 0.7626 (m) REVERT: A 740 MET cc_start: 0.7906 (tmm) cc_final: 0.7222 (tpp) REVERT: B 515 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: B 543 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7443 (t80) REVERT: B 873 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: C 34 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7175 (mmp80) REVERT: C 51 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8835 (p) REVERT: C 390 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7266 (tt) REVERT: H 105 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.7853 (p-90) REVERT: H 111 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6394 (t80) REVERT: L 49 TYR cc_start: 0.8263 (p90) cc_final: 0.7949 (p90) outliers start: 94 outliers final: 73 residues processed: 233 average time/residue: 0.1347 time to fit residues: 54.0979 Evaluate side-chains 238 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 155 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 111 TYR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [303, 148, 240, 96, 137, 157, 260, 16, 242, 247, 56] chunk 303 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 260 optimal weight: 0.0470 chunk 16 optimal weight: 0.0970 chunk 242 optimal weight: 1.9990 chunk 247 optimal weight: 0.0870 chunk 56 optimal weight: 0.4980 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.102099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.079362 restraints weight = 69106.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080164 restraints weight = 42891.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080636 restraints weight = 31036.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080898 restraints weight = 28562.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.081156 restraints weight = 24706.219| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25165 Z= 0.109 Angle : 0.621 11.871 34384 Z= 0.304 Chirality : 0.045 0.282 4086 Planarity : 0.004 0.071 4345 Dihedral : 4.398 28.052 3316 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.93 % Allowed : 21.27 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.15), residues: 3051 helix: 1.72 (0.21), residues: 631 sheet: -0.56 (0.19), residues: 685 loop : -1.54 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.016 0.001 TYR C 904 PHE 0.014 0.001 PHE A 238 TRP 0.038 0.002 TRP C 886 HIS 0.007 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (25082) covalent geometry : angle 0.60086 / 0.30 (34173) SS BOND : bond 0.00464 / 0.32 ( 38) SS BOND : angle 1.69149 / 1.19 ( 76) hydrogen bonds : bond 0.03685 / 2.50 ( 957) hydrogen bonds : angle 5.11225 / 3.50 ( 2583) link_BETA1-4 : bond 0.00839 / 0.58 ( 7) link_BETA1-4 : angle 1.94748 / 1.14 ( 21) link_NAG-ASN : bond 0.00377 / 0.21 ( 38) link_NAG-ASN : angle 2.31889 / 1.50 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 182 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6487 (t80) cc_final: 0.6217 (t80) REVERT: A 104 TRP cc_start: 0.7336 (m-90) cc_final: 0.6973 (m-90) REVERT: A 229 LEU cc_start: 0.7066 (mm) cc_final: 0.6828 (tp) REVERT: A 324 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7049 (pp20) REVERT: A 740 MET cc_start: 0.7775 (tmm) cc_final: 0.7162 (tpp) REVERT: B 469 SER cc_start: 0.8772 (t) cc_final: 0.8330 (p) REVERT: B 515 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: B 543 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7314 (t80) REVERT: B 873 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8444 (m-10) REVERT: C 34 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.6900 (mmp80) REVERT: C 51 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8772 (p) REVERT: H 48 MET cc_start: 0.7306 (mmp) cc_final: 0.5963 (mmm) REVERT: H 105 TRP cc_start: 0.8338 (OUTLIER) cc_final: 0.7781 (p-90) REVERT: L 24 ARG cc_start: 0.7688 (mtp180) cc_final: 0.6715 (mtm180) REVERT: L 49 TYR cc_start: 0.8178 (p90) cc_final: 0.7883 (p90) outliers start: 76 outliers final: 56 residues processed: 239 average time/residue: 0.1347 time to fit residues: 55.2612 Evaluate side-chains 225 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 162 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [211, 157, 63, 36, 79, 191, 134, 169, 136, 89, 207] chunk 211 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 36 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C1011 GLN C1101 HIS H 6 GLN L 27 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.100246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077366 restraints weight = 69152.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077979 restraints weight = 43800.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.078533 restraints weight = 31965.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078842 restraints weight = 28579.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078934 restraints weight = 26190.538| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25165 Z= 0.152 Angle : 0.645 11.717 34384 Z= 0.314 Chirality : 0.046 0.277 4086 Planarity : 0.004 0.074 4345 Dihedral : 4.443 28.124 3316 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.13 % Allowed : 21.27 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.15), residues: 3051 helix: 1.72 (0.21), residues: 631 sheet: -0.62 (0.19), residues: 693 loop : -1.51 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.023 0.001 TYR C 904 PHE 0.014 0.001 PHE H 70 TRP 0.038 0.002 TRP C 886 HIS 0.006 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (25082) covalent geometry : angle 0.62360 / 0.31 (34173) SS BOND : bond 0.00477 / 0.32 ( 38) SS BOND : angle 1.90117 / 1.32 ( 76) hydrogen bonds : bond 0.03944 / 2.70 ( 957) hydrogen bonds : angle 5.14072 / 3.53 ( 2583) link_BETA1-4 : bond 0.00832 / 0.58 ( 7) link_BETA1-4 : angle 1.95464 / 1.13 ( 21) link_NAG-ASN : bond 0.00389 / 0.22 ( 38) link_NAG-ASN : angle 2.37312 / 1.54 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 164 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6497 (t80) cc_final: 0.6221 (t80) REVERT: A 203 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7924 (mt) REVERT: A 229 LEU cc_start: 0.7136 (mm) cc_final: 0.6834 (tp) REVERT: A 324 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7052 (pp20) REVERT: A 543 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.6838 (t80) REVERT: A 740 MET cc_start: 0.8099 (tmm) cc_final: 0.7404 (tpp) REVERT: B 469 SER cc_start: 0.8796 (t) cc_final: 0.8355 (p) REVERT: B 515 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: B 543 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7414 (t80) REVERT: B 873 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8538 (m-10) REVERT: C 34 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7126 (mmp80) REVERT: C 51 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8824 (p) REVERT: H 37 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7547 (m) REVERT: H 48 MET cc_start: 0.7546 (mmp) cc_final: 0.6065 (mmm) REVERT: H 105 TRP cc_start: 0.8414 (OUTLIER) cc_final: 0.7824 (p-90) REVERT: L 24 ARG cc_start: 0.7663 (mtp180) cc_final: 0.6752 (mtm180) REVERT: L 49 TYR cc_start: 0.8254 (p90) cc_final: 0.7974 (p90) outliers start: 81 outliers final: 64 residues processed: 226 average time/residue: 0.1392 time to fit residues: 53.5471 Evaluate side-chains 231 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 157 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [220, 35, 304, 9, 52, 124, 274, 184, 137, 240, 48] chunk 220 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 274 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 240 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.100158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077265 restraints weight = 69259.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077987 restraints weight = 43249.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.078310 restraints weight = 31678.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078618 restraints weight = 30272.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078804 restraints weight = 26084.050| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 25165 Z= 0.207 Angle : 0.796 59.199 34384 Z= 0.428 Chirality : 0.046 0.277 4086 Planarity : 0.004 0.073 4345 Dihedral : 4.460 28.119 3316 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.09 % Allowed : 21.30 % Favored : 75.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 3051 helix: 1.71 (0.21), residues: 631 sheet: -0.63 (0.19), residues: 694 loop : -1.52 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.035 0.001 TYR H 111 PHE 0.013 0.001 PHE H 70 TRP 0.045 0.003 TRP H 36 HIS 0.005 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (25082) covalent geometry : angle 0.77661 / 0.42 (34173) SS BOND : bond 0.00485 / 0.32 ( 38) SS BOND : angle 2.38638 / 1.40 ( 76) hydrogen bonds : bond 0.03969 / 2.72 ( 957) hydrogen bonds : angle 5.14236 / 3.53 ( 2583) link_BETA1-4 : bond 0.00984 / 0.68 ( 7) link_BETA1-4 : angle 1.97886 / 1.15 ( 21) link_NAG-ASN : bond 0.00396 / 0.22 ( 38) link_NAG-ASN : angle 2.37148 / 1.54 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3333.92 seconds wall clock time: 58 minutes 51.71 seconds (3531.71 seconds total)