Starting phenix.real_space_refine on Sat Feb 7 19:50:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xod_33345/02_2026/7xod_33345.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xod_33345/02_2026/7xod_33345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xod_33345/02_2026/7xod_33345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xod_33345/02_2026/7xod_33345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xod_33345/02_2026/7xod_33345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xod_33345/02_2026/7xod_33345.map" } resolution = 3.27 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= 0.001 sd= 0.022 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 151 5.16 5 C 22977 2.51 5 N 5979 2.21 5 O 7066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 196 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36173 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7685 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 349 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 9, 'ASN:plan1': 5, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 183 Chain: "B" Number of atoms: 7681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7681 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 7 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 5, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 186 Chain: "C" Number of atoms: 7709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7709 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ASP:plan': 9, 'GLN:plan1': 10, 'ASN:plan1': 9, 'GLU:plan': 9, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 191 Chain: "X" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1633 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1622 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 201} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Z" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1641 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1611 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "R" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1652 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1622 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 201} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" 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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" 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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Restraints were copied for chains: E Time building chain proxies: 8.01, per 1000 atoms: 0.22 Number of scatterers: 36173 At special positions: 0 Unit cell: (222.48, 167.272, 231.544, 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 151 16.00 O 7066 8.00 N 5979 7.00 C 22977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=1.68 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 480 " - pdb=" SG CYS A 488 " 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.38 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.15 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=2.23 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=1.88 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 150 " - pdb=" SG CYS X 206 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 134 " - pdb=" SG CYS Y 194 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 31 " - pdb=" SG CYS Z 105 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 150 " - pdb=" SG CYS U 206 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS V 134 " - pdb=" SG CYS V 194 " distance=1.99 Simple disulfide: pdb=" SG CYS W 31 " - pdb=" SG CYS W 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.38 Simple disulfide: pdb=" SG CYS R 150 " - pdb=" SG CYS R 206 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 194 " distance=2.03 Simple disulfide: pdb=" SG CYS T 31 " - pdb=" SG CYS T 105 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B1134 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 801 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8812 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 77 sheets defined 19.8% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.754A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.900A pdb=" N HIS A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.675A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.524A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.594A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.159A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.882A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.540A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.106A 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 984 removed outlier: 3.553A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.731A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (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 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.564A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 4.016A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.532A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.508A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.552A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.589A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.905A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.770A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.757A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.857A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.464A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.767A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.676A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.518A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.468A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.702A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.661A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.010A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.876A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.519A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.996A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.717A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 removed outlier: 3.712A pdb=" N THR X 91 " --> pdb=" O SER X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 137 through 141 removed outlier: 3.554A pdb=" N SER X 140 " --> pdb=" O SER X 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 171 removed outlier: 3.587A pdb=" N LEU X 169 " --> pdb=" O SER X 166 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR X 170 " --> pdb=" O GLY X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 199 No H-bonds generated for 'chain 'X' and resid 197 through 199' Processing helix chain 'Y' and resid 79 through 83 Processing helix chain 'Y' and resid 121 through 128 removed outlier: 3.634A pdb=" N LEU Y 125 " --> pdb=" O SER Y 121 " (cutoff:3.500A) Processing helix chain 'Y' and resid 149 through 153 Processing helix chain 'Y' and resid 183 through 189 removed outlier: 3.821A pdb=" N HIS Y 189 " --> pdb=" O ASP Y 185 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 41 Processing helix chain 'Z' and resid 71 through 74 removed outlier: 3.633A pdb=" N GLN Z 74 " --> pdb=" O ASP Z 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 71 through 74' Processing helix chain 'U' and resid 87 through 91 removed outlier: 3.595A pdb=" N THR U 91 " --> pdb=" O SER U 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 103 removed outlier: 3.673A pdb=" N SER U 103 " --> pdb=" O ALA U 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 100 through 103' Processing helix chain 'U' and resid 137 through 141 Processing helix chain 'U' and resid 197 through 199 No H-bonds generated for 'chain 'U' and resid 197 through 199' Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.737A pdb=" N ILE V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 126 Processing helix chain 'V' and resid 150 through 153 Processing helix chain 'V' and resid 183 through 189 removed outlier: 4.000A pdb=" N HIS V 189 " --> pdb=" O ASP V 185 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 41 Processing helix chain 'W' and resid 96 through 100 Processing helix chain 'R' and resid 28 through 32 Processing helix chain 'R' and resid 87 through 91 removed outlier: 3.851A pdb=" N THR R 91 " --> pdb=" O SER R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 199 Processing helix chain 'S' and resid 121 through 128 removed outlier: 3.606A pdb=" N LEU S 125 " --> pdb=" O SER S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 153 Processing helix chain 'S' and resid 182 through 189 removed outlier: 3.769A pdb=" N TYR S 186 " --> pdb=" O SER S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 41 removed outlier: 4.234A pdb=" N ARG T 40 " --> pdb=" O THR T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 75 removed outlier: 4.078A pdb=" N GLN T 74 " --> pdb=" O ASP T 71 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLY T 75 " --> pdb=" O SER T 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 71 through 75' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.844A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.200A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.495A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.382A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.622A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.232A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.051A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.617A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.968A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.303A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.722A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.507A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.913A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.439A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.987A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.594A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.585A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.746A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.631A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.982A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 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 654 through 655 removed outlier: 6.054A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.535A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.116A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.541A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.886A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.612A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.674A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.674A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.345A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.074A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.894A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.894A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.230A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.507A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.873A pdb=" N THR X 69 " --> pdb=" O GLU X 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.411A pdb=" N GLU X 10 " --> pdb=" O THR X 120 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ARG X 50 " --> pdb=" O ILE X 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP X 36 " --> pdb=" O MET X 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 130 through 132 removed outlier: 4.154A pdb=" N PHE X 132 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU X 151 " --> pdb=" O PHE X 132 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR X 186 " --> pdb=" O ASP X 154 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER X 189 " --> pdb=" O PHE X 176 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE X 176 " --> pdb=" O SER X 189 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 161 through 164 Processing sheet with id=AF2, first strand: chain 'Y' and resid 4 through 5 removed outlier: 5.109A pdb=" N THR Y 69 " --> pdb=" O ALA Y 25 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N GLN Y 27 " --> pdb=" O SER Y 67 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N SER Y 67 " --> pdb=" O GLN Y 27 " (cutoff:3.500A) removed outlier: 11.104A pdb=" N ILE Y 29 " --> pdb=" O SER Y 65 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N SER Y 65 " --> pdb=" O ILE Y 29 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 45 through 48 removed outlier: 6.148A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN Y 38 " --> pdb=" O THR Y 85 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN Y 90 " --> pdb=" O THR Y 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR Y 97 " --> pdb=" O GLN Y 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 45 through 48 removed outlier: 6.148A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN Y 38 " --> pdb=" O THR Y 85 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 114 through 118 removed outlier: 3.815A pdb=" N ASN Y 138 " --> pdb=" O TYR Y 173 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR Y 173 " --> pdb=" O ASN Y 138 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 191 through 196 Processing sheet with id=AF7, first strand: chain 'Z' and resid 14 through 16 removed outlier: 3.558A pdb=" N SER Z 30 " --> pdb=" O SER Z 16 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR Z 78 " --> pdb=" O GLN Z 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 19 through 21 removed outlier: 6.090A pdb=" N GLY Z 19 " --> pdb=" O THR Z 127 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP Z 120 " --> pdb=" O ILE Z 107 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE Z 107 " --> pdb=" O TRP Z 120 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN Z 122 " --> pdb=" O CYS Z 105 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 58 through 59 Processing sheet with id=AG1, first strand: chain 'U' and resid 5 through 6 removed outlier: 3.955A pdb=" N VAL U 5 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR U 78 " --> pdb=" O ASP U 73 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 10 through 12 removed outlier: 7.304A pdb=" N ILE U 34 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ARG U 50 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 130 through 133 removed outlier: 6.085A pdb=" N TYR U 186 " --> pdb=" O ASP U 154 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 130 through 133 removed outlier: 6.085A pdb=" N TYR U 186 " --> pdb=" O ASP U 154 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL U 179 " --> pdb=" O SER U 187 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'U' and resid 160 through 164 Processing sheet with id=AG6, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.558A pdb=" N VAL V 104 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA V 84 " --> pdb=" O VAL V 104 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP V 50 " --> pdb=" O ASN V 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.558A pdb=" N VAL V 104 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA V 84 " --> pdb=" O VAL V 104 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR V 97 " --> pdb=" O GLN V 90 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 114 through 118 removed outlier: 3.525A pdb=" N PHE V 118 " --> pdb=" O VAL V 133 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL V 133 " --> pdb=" O PHE V 118 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N TYR V 173 " --> pdb=" O ASN V 138 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 144 through 148 Processing sheet with id=AH2, first strand: chain 'W' and resid 12 through 14 Processing sheet with id=AH3, first strand: chain 'W' and resid 68 through 69 removed outlier: 6.796A pdb=" N PHE W 56 " --> pdb=" O ARG W 47 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ARG W 47 " --> pdb=" O PHE W 56 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA W 58 " --> pdb=" O TRP W 45 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET W 43 " --> pdb=" O ALA W 60 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA W 42 " --> pdb=" O ASP W 108 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 80 through 82 removed outlier: 3.679A pdb=" N THR W 87 " --> pdb=" O ASP W 82 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AH6, first strand: chain 'R' and resid 58 through 59 removed outlier: 4.219A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 132 through 134 removed outlier: 3.733A pdb=" N CYS R 150 " --> pdb=" O SER R 190 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER R 190 " --> pdb=" O CYS R 150 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 162 through 163 Processing sheet with id=AH9, first strand: chain 'S' and resid 4 through 5 removed outlier: 3.614A pdb=" N ASP S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.533A pdb=" N THR S 102 " --> pdb=" O TYR S 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU S 47 " --> pdb=" O TRP S 35 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN S 37 " --> pdb=" O LYS S 45 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 114 through 118 removed outlier: 3.714A pdb=" N ALA S 130 " --> pdb=" O LEU S 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS S 134 " --> pdb=" O SER S 177 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR S 173 " --> pdb=" O ASN S 138 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN S 160 " --> pdb=" O THR S 178 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'S' and resid 192 through 196 removed outlier: 3.611A pdb=" N LYS S 207 " --> pdb=" O CYS S 194 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'T' and resid 13 through 16 removed outlier: 3.542A pdb=" N SER T 16 " --> pdb=" O SER T 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER T 30 " --> pdb=" O SER T 16 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'T' and resid 19 through 21 removed outlier: 5.083A pdb=" N ASP T 118 " --> pdb=" O SER T 109 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER T 109 " --> pdb=" O ASP T 118 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP T 120 " --> pdb=" O ILE T 107 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE T 107 " --> pdb=" O TRP T 120 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN T 122 " --> pdb=" O CYS T 105 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET T 43 " --> pdb=" O VAL T 59 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL T 59 " --> pdb=" O MET T 43 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP T 45 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE T 68 " --> pdb=" O VAL T 59 " (cutoff:3.500A) 1416 hydrogen bonds defined for protein. 3756 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: 9.58 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6036 1.32 - 1.45: 10521 1.45 - 1.58: 20249 1.58 - 1.70: 0 1.70 - 1.83: 191 Bond restraints: 36997 Sorted by residual: bond pdb=" CA SER A 359 " pdb=" CB SER A 359 " ideal model delta sigma weight residual 1.535 1.483 0.051 1.32e-02 5.74e+03 1.52e+01 bond pdb=" C GLU R 158 " pdb=" N PRO R 159 " ideal model delta sigma weight residual 1.328 1.373 -0.044 1.26e-02 6.30e+03 1.24e+01 bond pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.22e-02 6.72e+03 1.18e+01 bond pdb=" N LEU R 151 " pdb=" CA LEU R 151 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.25e-02 6.40e+03 9.28e+00 bond pdb=" N TYR U 155 " pdb=" CA TYR U 155 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.23e-02 6.61e+03 9.16e+00 ... (remaining 36992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 48990 1.55 - 3.11: 1181 3.11 - 4.66: 249 4.66 - 6.21: 24 6.21 - 7.77: 11 Bond angle restraints: 50455 Sorted by residual: angle pdb=" C PRO C 209 " pdb=" CA PRO C 209 " pdb=" CB PRO C 209 " ideal model delta sigma weight residual 111.40 103.63 7.77 1.54e+00 4.22e-01 2.54e+01 angle pdb=" CA GLU R 158 " pdb=" C GLU R 158 " pdb=" N PRO R 159 " ideal model delta sigma weight residual 116.90 124.12 -7.22 1.50e+00 4.44e-01 2.32e+01 angle pdb=" N CYS A 361 " pdb=" CA CYS A 361 " pdb=" C CYS A 361 " ideal model delta sigma weight residual 108.52 115.76 -7.24 1.52e+00 4.33e-01 2.27e+01 angle pdb=" O LEU A 335 " pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 123.19 128.62 -5.43 1.17e+00 7.31e-01 2.16e+01 angle pdb=" CA CYS V 134 " pdb=" C CYS V 134 " pdb=" O CYS V 134 " ideal model delta sigma weight residual 121.66 116.06 5.60 1.22e+00 6.72e-01 2.10e+01 ... (remaining 50450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20381 17.95 - 35.90: 1568 35.90 - 53.84: 335 53.84 - 71.79: 81 71.79 - 89.74: 34 Dihedral angle restraints: 22399 sinusoidal: 8678 harmonic: 13721 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -151.79 65.79 1 1.00e+01 1.00e-02 5.66e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 27.29 65.71 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS V 134 " pdb=" SG CYS V 134 " pdb=" SG CYS V 194 " pdb=" CB CYS V 194 " ideal model delta sinusoidal sigma weight residual 93.00 153.38 -60.38 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 22396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 5389 0.093 - 0.186: 481 0.186 - 0.279: 14 0.279 - 0.372: 1 0.372 - 0.465: 1 Chirality restraints: 5886 Sorted by residual: chirality pdb=" CB VAL C 70 " pdb=" CA VAL C 70 " pdb=" CG1 VAL C 70 " pdb=" CG2 VAL C 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA VAL R 152 " pdb=" N VAL R 152 " pdb=" C VAL R 152 " pdb=" CB VAL R 152 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 5883 not shown) Planarity restraints: 6517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1312 " 0.193 2.00e-02 2.50e+03 1.59e-01 3.17e+02 pdb=" C7 NAG B1312 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG B1312 " 0.141 2.00e-02 2.50e+03 pdb=" N2 NAG B1312 " -0.257 2.00e-02 2.50e+03 pdb=" O7 NAG B1312 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 357 " -0.025 2.00e-02 2.50e+03 5.16e-02 2.66e+01 pdb=" C ARG A 357 " 0.089 2.00e-02 2.50e+03 pdb=" O ARG A 357 " -0.034 2.00e-02 2.50e+03 pdb=" N ILE A 358 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1133 " -0.022 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C VAL B1133 " 0.078 2.00e-02 2.50e+03 pdb=" O VAL B1133 " -0.030 2.00e-02 2.50e+03 pdb=" N ASN B1134 " -0.026 2.00e-02 2.50e+03 ... (remaining 6514 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 25 2.35 - 2.99: 19708 2.99 - 3.63: 51161 3.63 - 4.26: 79414 4.26 - 4.90: 134024 Nonbonded interactions: 284332 Sorted by model distance: nonbonded pdb=" OD1 ASP T 108 " pdb=" OD1 ASP T 118 " model vdw 1.716 3.040 nonbonded pdb=" OE1 GLN S 6 " pdb=" O THR S 22 " model vdw 1.977 3.040 nonbonded pdb=" CG ASP T 108 " pdb=" OD1 ASP T 118 " model vdw 2.005 3.270 nonbonded pdb=" NE2 GLN S 6 " pdb=" CB CYS S 23 " model vdw 2.148 3.520 nonbonded pdb=" O GLY A1099 " pdb=" OG1 THR A1100 " model vdw 2.175 3.040 ... (remaining 284327 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 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 70 or resid 81 through 86 or (resid 87 and (name N or name CA or n \ ame C or name O or name CB )) or resid 88 through 96 or (resid 97 through 98 and \ (name N or name CA or name C or name O or name CB )) or resid 99 through 114 or \ (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 6 through 133 or (resid 134 and (name N or name CA or name C or name O or name C \ B )) or resid 135 through 136 or (resid 137 and (name N or name CA or name C or \ name O or name CB )) or resid 138 through 160 or (resid 161 through 164 and (nam \ e N or name CA or name C or name O or name CB )) or resid 165 through 253 or (re \ sid 254 and (name N or name CA or name C or name O or name CB )) or resid 255 th \ rough 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 355 or (resid 356 through 357 and (name N or name CA or na \ me C or name O or name CB )) or resid 358 through 387 or (resid 388 and (name N \ or name CA or name C or name O or name CB )) or resid 389 through 453 or (resid \ 454 and (name N or name CA or name C or name O or name CB )) or resid 455 throug \ h 458 or (resid 459 and (name N or name CA or name C or name O or name CB )) or \ resid 460 through 553 or (resid 554 and (name N or name CA or name C or name O o \ r name CB )) or resid 555 or (resid 556 through 558 and (name N or name CA or na \ me C or name O or name CB )) or resid 559 through 563 or (resid 564 and (name N \ or name CA or name C or name O or name CB )) or resid 565 through 570 or (resid \ 571 through 572 and (name N or name CA or name C or name O or name CB )) or resi \ d 573 through 620 or resid 641 through 676 or (resid 690 and (name N or name CA \ or name C or name O or name CB )) or resid 691 through 747 or (resid 748 and (na \ me N or name CA or name C or name O or name CB )) or resid 749 through 827 or (r \ esid 828 and (name N or name CA or name C or name O or name CB )) or resid 855 t \ hrough 984 or (resid 985 and (name N or name CA or name C or name O or name CB ) \ ) or resid 986 through 987 or (resid 988 through 989 and (name N or name CA or n \ ame C or name O or name CB )) or resid 990 through 993 or (resid 994 and (name N \ or name CA or name C or name O or name CB )) or resid 995 through 1037 or (resi \ d 1038 and (name N or name CA or name C or name O or name CB )) or resid 1039 th \ rough 1050 or (resid 1051 and (name N or name CA or name C or name O or name CB \ )) or resid 1052 through 1110 or (resid 1111 and (name N or name CA or name C or \ name O or name CB )) or resid 1112 through 1143 or (resid 1144 through 1146 and \ (name N or name CA or name C or name O or name CB )) or resid 1301 through 1311 \ )) selection = (chain 'B' and (resid 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 86 or (resid 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 96 or (resid 97 through 98 and (name N or name CA or \ name C or name O or name CB )) or resid 99 through 114 or (resid 115 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 133 or (resid \ 134 and (name N or name CA or name C or name O or name CB )) or resid 135 throu \ gh 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 through 160 or (resid 161 through 164 and (name N or name CA or name \ C or name O or name CB )) or resid 165 through 253 or (resid 254 and (name N or \ name CA or name C or name O or name CB )) or resid 255 through 318 or (resid 319 \ and (name N or name CA or name C or name O or name CB )) or resid 320 through 3 \ 31 or (resid 332 and (name N or name CA or name C or name O or name CB )) or res \ id 333 through 355 or (resid 356 through 357 and (name N or name CA or name C or \ name O or name CB )) or resid 358 through 387 or (resid 388 and (name N or name \ CA or name C or name O or name CB )) or resid 389 through 453 or (resid 454 and \ (name N or name CA or name C or name O or name CB )) or resid 455 through 458 o \ r (resid 459 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 60 through 553 or (resid 554 and (name N or name CA or name C or name O or name \ CB )) or resid 555 or (resid 556 through 558 and (name N or name CA or name C or \ name O or name CB )) or resid 559 through 563 or (resid 564 and (name N or name \ CA or name C or name O or name CB )) or resid 565 through 570 or (resid 571 thr \ ough 572 and (name N or name CA or name C or name O or name CB )) or resid 573 t \ hrough 620 or resid 641 through 676 or (resid 690 and (name N or name CA or name \ C or name O or name CB )) or resid 691 through 747 or (resid 748 and (name N or \ name CA or name C or name O or name CB )) or resid 749 through 827 or (resid 82 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 855 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or re \ sid 986 through 987 or (resid 988 through 989 and (name N or name CA or name C o \ r name O or name CB )) or resid 990 through 1037 or (resid 1038 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1039 through 1050 or (resid 10 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 1052 throug \ h 1110 or (resid 1111 and (name N or name CA or name C or name O or name CB )) o \ r resid 1112 through 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1301 through 1311)) 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 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 69 through 70 or resid 81 throug \ h 107 or (resid 108 through 113 and (name N or name CA or name C or name O or na \ me CB )) or resid 114 through 175 or (resid 176 through 187 and (name N or name \ CA or name C or name O or name CB )) or resid 188 through 199 or (resid 200 and \ (name N or name CA or name C or name O or name CB )) or resid 201 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 248 or (resid 249 through 250 and (name N or name CA o \ r name C or name O or name CB )) or resid 251 through 303 or (resid 304 and (nam \ e N or name CA or name C or name O or name CB )) or resid 305 through 320 or (re \ sid 321 and (name N or name CA or name C or name O or name CB )) or resid 322 th \ rough 368 or (resid 369 and (name N or name CA or name C or name O or name CB )) \ or resid 370 through 402 or (resid 403 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 405 or (resid 406 and (name N or name CA o \ r name C or name O or name CB )) or resid 407 through 423 or (resid 424 and (nam \ e N or name CA or name C or name O or name CB )) or resid 425 through 427 or (re \ sid 428 and (name N or name CA or name C or name O or name CB )) or resid 429 th \ rough 438 or (resid 439 and (name N or name CA or name C or name O or name CB )) \ or resid 440 through 441 or (resid 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 or (resid 444 through 445 and (name N or name CA o \ r name C or name O or name CB )) or resid 446 through 461 or (resid 462 and (nam \ e N or name CA or name C or name O or name CB )) or resid 463 through 508 or (re \ sid 509 and (name N or name CA or name C or name O or name CB )) or resid 510 th \ rough 556 or (resid 557 through 558 and (name N or name CA or name C or name O o \ r name CB )) or resid 559 through 568 or (resid 569 through 572 and (name N or n \ ame CA or name C or name O or name CB )) or resid 573 through 662 or (resid 663 \ and (name N or name CA or name C or name O or name CB )) or resid 664 through 70 \ 1 or (resid 702 and (name N or name CA or name C or name O or name CB )) or resi \ d 703 through 739 or (resid 740 and (name N or name CA or name C or name O or na \ me CB )) or resid 741 through 794 or (resid 795 and (name N or name CA or name C \ or name O or name CB )) or resid 796 through 807 or (resid 808 and (name N or n \ ame CA or name C or name O or name CB )) or resid 809 through 818 or (resid 819 \ and (name N or name CA or name C or name O or name CB )) or resid 820 through 82 \ 4 or (resid 825 and (name N or name CA or name C or name O or name CB )) or resi \ d 826 through 917 or (resid 918 and (name N or name CA or name C or name O or na \ me CB )) or resid 919 through 946 or (resid 947 and (name N or name CA or name C \ or name O or name CB )) or resid 948 through 963 or (resid 964 and (name N or n \ ame CA or name C or name O or name CB )) or resid 965 through 993 or (resid 994 \ and (name N or name CA or name C or name O or name CB )) or resid 995 through 10 \ 72 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or re \ sid 1074 through 1137 or (resid 1138 and (name N or name CA or name C or name O \ or name CB )) or resid 1139 through 1140 or (resid 1141 through 1142 and (name N \ or name CA or name C or name O or name CB )) or resid 1143 through 1145 or (res \ id 1146 and (name N or name CA or name C or name O or name CB )) or resid 1301 t \ hrough 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'R' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 72 or (resid 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 through 133 or (r \ esid 134 through 135 and (name N or name CA or name C or name O or name CB )) or \ resid 136 through 156 or resid 160 through 173 or (resid 174 and (name N or nam \ e CA or name C or name O or name CB )) or resid 175 through 225)) selection = (chain 'U' and (resid 1 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 through 156 or resid 160 throu \ gh 225)) selection = (chain 'X' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 173 or (resid 174 and (name N or name CA or name C or name O or name CB )) \ or resid 175 through 225)) } ncs_group { reference = (chain 'S' and (resid 1 through 7 or resid 9 through 32 or (resid 33 through 34 \ and (name N or name CA or name C or name O or name CB )) or resid 35 through 104 \ or (resid 105 and (name N or name CA or name C or name O or name CB )) or resid \ 106 through 107 or (resid 108 and (name N or name CA or name C or name O or nam \ e CB )) or resid 109 through 130 or (resid 131 and (name N or name CA or name C \ or name O or name CB )) or resid 132 through 139 or resid 141 through 213)) selection = (chain 'V' and (resid 1 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 104 or (resid 105 and (name N or na \ me CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 a \ nd (name N or name CA or name C or name O or name CB )) or resid 109 through 130 \ or (resid 131 and (name N or name CA or name C or name O or name CB )) or resid \ 132 through 144 or (resid 145 and (name N or name CA or name C or name O or nam \ e CB )) or resid 146 through 213)) selection = (chain 'Y' and (resid 1 through 7 or resid 9 through 32 or (resid 33 through 34 \ and (name N or name CA or name C or name O or name CB )) or resid 35 through 48 \ or (resid 49 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 0 through 139 or resid 141 through 144 or (resid 145 and (name N or name CA or n \ ame C or name O or name CB )) or resid 146 through 213)) } ncs_group { reference = (chain 'T' and (resid 10 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 129)) selection = (chain 'W' and (resid 10 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 129)) selection = chain 'Z' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 33.880 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 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 : 0.005 0.353 37090 Z= 0.250 Angle : 0.786 61.832 50680 Z= 0.423 Chirality : 0.046 0.465 5886 Planarity : 0.004 0.159 6480 Dihedral : 13.941 89.739 13425 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.16 % Allowed : 9.20 % Favored : 90.64 % Cbeta Deviations : 0.02 % 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: -2.45 (0.11), residues: 4666 helix: 0.30 (0.19), residues: 682 sheet: -1.44 (0.12), residues: 1341 loop : -2.32 (0.10), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Z 54 TYR 0.018 0.001 TYR U 155 PHE 0.014 0.001 PHE A 347 TRP 0.010 0.001 TRP B 353 HIS 0.003 0.000 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00314 (36997) covalent geometry : angle 0.60330 (50455) SS BOND : bond 0.09027 ( 54) SS BOND : angle 10.56246 ( 108) hydrogen bonds : bond 0.18374 ( 1384) hydrogen bonds : angle 8.02152 ( 3756) link_BETA1-4 : bond 0.00524 ( 2) link_BETA1-4 : angle 2.09036 ( 6) link_NAG-ASN : bond 0.00500 ( 37) link_NAG-ASN : angle 2.75546 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 698 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.7484 (mt) cc_final: 0.7195 (mp) REVERT: A 308 VAL cc_start: 0.8149 (t) cc_final: 0.7841 (m) REVERT: A 564 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7308 (mm-40) REVERT: A 576 VAL cc_start: 0.8548 (m) cc_final: 0.8338 (t) REVERT: A 975 SER cc_start: 0.8194 (p) cc_final: 0.7757 (t) REVERT: A 1084 ASP cc_start: 0.7476 (t0) cc_final: 0.6840 (t0) REVERT: A 1105 THR cc_start: 0.8144 (t) cc_final: 0.7899 (p) REVERT: B 51 THR cc_start: 0.8434 (t) cc_final: 0.8052 (p) REVERT: B 169 GLU cc_start: 0.6350 (mp0) cc_final: 0.5954 (mp0) REVERT: B 281 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6019 (tm-30) REVERT: B 282 ASN cc_start: 0.7343 (m-40) cc_final: 0.7129 (m-40) REVERT: B 605 SER cc_start: 0.7770 (p) cc_final: 0.7485 (p) REVERT: B 698 SER cc_start: 0.8548 (t) cc_final: 0.8234 (p) REVERT: B 773 GLU cc_start: 0.6039 (tt0) cc_final: 0.5812 (tt0) REVERT: B 970 PHE cc_start: 0.8351 (m-80) cc_final: 0.8111 (m-80) REVERT: B 973 ILE cc_start: 0.8717 (tt) cc_final: 0.8471 (tt) REVERT: B 983 ARG cc_start: 0.7309 (mtm110) cc_final: 0.7096 (ttp80) REVERT: B 990 GLU cc_start: 0.7548 (tp30) cc_final: 0.7116 (tp30) REVERT: B 1084 ASP cc_start: 0.7458 (t0) cc_final: 0.7099 (t0) REVERT: B 1091 ARG cc_start: 0.7451 (mtt180) cc_final: 0.6305 (mtt180) REVERT: C 54 LEU cc_start: 0.7960 (mt) cc_final: 0.7749 (mp) REVERT: C 290 ASP cc_start: 0.7307 (t0) cc_final: 0.7000 (t0) REVERT: C 317 ASN cc_start: 0.7251 (m-40) cc_final: 0.6986 (m-40) REVERT: C 383 SER cc_start: 0.7906 (t) cc_final: 0.7543 (m) REVERT: C 398 ASP cc_start: 0.7497 (m-30) cc_final: 0.6720 (m-30) REVERT: C 406 GLU cc_start: 0.6792 (tt0) cc_final: 0.6515 (tt0) REVERT: C 440 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7786 (mmtm) REVERT: C 498 ARG cc_start: 0.7216 (mtt90) cc_final: 0.6846 (mtt90) REVERT: C 574 ASP cc_start: 0.7520 (t70) cc_final: 0.7132 (t0) REVERT: C 670 ILE cc_start: 0.8229 (mm) cc_final: 0.7947 (mt) REVERT: C 945 LEU cc_start: 0.7716 (mm) cc_final: 0.7503 (mp) REVERT: C 964 LYS cc_start: 0.8315 (tttt) cc_final: 0.8031 (tttm) REVERT: C 1105 THR cc_start: 0.8214 (t) cc_final: 0.7927 (t) REVERT: X 81 MET cc_start: 0.4886 (tmm) cc_final: 0.4407 (tmm) REVERT: X 122 SER cc_start: 0.5429 (t) cc_final: 0.5180 (p) REVERT: U 70 ILE cc_start: 0.5986 (tp) cc_final: 0.5782 (tp) REVERT: U 81 MET cc_start: 0.6720 (tpp) cc_final: 0.5977 (tpt) REVERT: V 31 SER cc_start: 0.8102 (m) cc_final: 0.7858 (p) REVERT: V 53 ASN cc_start: 0.5434 (t0) cc_final: 0.5199 (t0) REVERT: V 97 THR cc_start: 0.6490 (p) cc_final: 0.6272 (m) REVERT: R 118 MET cc_start: 0.1037 (tpt) cc_final: -0.0377 (tpt) outliers start: 6 outliers final: 3 residues processed: 702 average time/residue: 0.1975 time to fit residues: 231.0750 Evaluate side-chains 581 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 578 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 0.0970 chunk 455 optimal weight: 40.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 470 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 239 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 784 GLN A 901 GLN A 955 ASN A 957 GLN B 207 HIS B 317 ASN B 481 ASN B 506 GLN B 710 ASN B 856 ASN B 907 ASN B 949 GLN B 955 ASN B1005 GLN B1010 GLN C 99 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 784 GLN C 804 GLN C 856 ASN C 913 GLN C1054 GLN X 59 ASN X 210 HIS X 214 ASN Y 53 ASN Z 86 ASN U 6 GLN U 181 GLN U 202 GLN V 189 HIS W 48 GLN R 202 GLN R 210 HIS S 6 GLN S 124 GLN S 155 GLN S 199 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.214017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.154145 restraints weight = 61112.690| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.57 r_work: 0.3590 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37090 Z= 0.163 Angle : 0.643 15.835 50680 Z= 0.331 Chirality : 0.047 0.232 5886 Planarity : 0.005 0.047 6480 Dihedral : 5.678 59.933 5870 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.13 % Allowed : 14.70 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.35 (0.12), residues: 4666 helix: 1.55 (0.20), residues: 674 sheet: -0.72 (0.13), residues: 1372 loop : -1.70 (0.11), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 211 TYR 0.032 0.002 TYR B 265 PHE 0.020 0.002 PHE B 823 TRP 0.017 0.001 TRP V 35 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00374 (36997) covalent geometry : angle 0.62923 (50455) SS BOND : bond 0.00465 ( 54) SS BOND : angle 1.88902 ( 108) hydrogen bonds : bond 0.04171 ( 1384) hydrogen bonds : angle 6.07794 ( 3756) link_BETA1-4 : bond 0.00617 ( 2) link_BETA1-4 : angle 1.92621 ( 6) link_NAG-ASN : bond 0.00900 ( 37) link_NAG-ASN : angle 2.27410 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 582 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8809 (mt) cc_final: 0.8581 (mp) REVERT: A 54 LEU cc_start: 0.7977 (mt) cc_final: 0.7729 (mp) REVERT: A 319 ARG cc_start: 0.8320 (ttp80) cc_final: 0.8086 (ptm-80) REVERT: A 452 LEU cc_start: 0.1330 (OUTLIER) cc_final: 0.1089 (pp) REVERT: A 546 LEU cc_start: 0.8388 (tp) cc_final: 0.8130 (tt) REVERT: A 574 ASP cc_start: 0.8054 (m-30) cc_final: 0.7848 (m-30) REVERT: A 602 THR cc_start: 0.8345 (p) cc_final: 0.8016 (m) REVERT: A 975 SER cc_start: 0.8693 (p) cc_final: 0.8349 (t) REVERT: A 1054 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8021 (mm110) REVERT: A 1072 GLU cc_start: 0.8432 (pm20) cc_final: 0.8137 (pm20) REVERT: A 1084 ASP cc_start: 0.7992 (t0) cc_final: 0.7434 (t0) REVERT: B 51 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8220 (p) REVERT: B 58 PHE cc_start: 0.8091 (m-10) cc_final: 0.7885 (m-10) REVERT: B 196 ASN cc_start: 0.7523 (t0) cc_final: 0.7099 (t0) REVERT: B 266 TYR cc_start: 0.8004 (m-10) cc_final: 0.7763 (m-80) REVERT: B 276 LEU cc_start: 0.8497 (tp) cc_final: 0.8159 (tt) REVERT: B 281 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7087 (tm-30) REVERT: B 282 ASN cc_start: 0.8324 (m-40) cc_final: 0.7891 (m-40) REVERT: B 524 VAL cc_start: 0.4948 (OUTLIER) cc_final: 0.4582 (m) REVERT: B 645 THR cc_start: 0.8383 (m) cc_final: 0.8050 (p) REVERT: B 656 VAL cc_start: 0.8474 (t) cc_final: 0.8268 (m) REVERT: B 658 ASN cc_start: 0.8124 (m-40) cc_final: 0.7918 (p0) REVERT: B 698 SER cc_start: 0.8850 (t) cc_final: 0.8446 (p) REVERT: B 720 ILE cc_start: 0.8683 (mm) cc_final: 0.8474 (mt) REVERT: B 856 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8017 (p0) REVERT: B 900 MET cc_start: 0.8210 (mtt) cc_final: 0.7918 (mtp) REVERT: B 967 SER cc_start: 0.8343 (t) cc_final: 0.8064 (t) REVERT: B 969 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8456 (mtpt) REVERT: B 973 ILE cc_start: 0.8889 (tt) cc_final: 0.8654 (tt) REVERT: B 998 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8335 (p) REVERT: C 190 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.7979 (ptp90) REVERT: C 205 SER cc_start: 0.8604 (p) cc_final: 0.8347 (m) REVERT: C 234 ASN cc_start: 0.3316 (OUTLIER) cc_final: 0.3058 (t0) REVERT: C 269 TYR cc_start: 0.7999 (m-80) cc_final: 0.7782 (m-80) REVERT: C 317 ASN cc_start: 0.8003 (m-40) cc_final: 0.7703 (m-40) REVERT: C 347 PHE cc_start: 0.8460 (m-10) cc_final: 0.8243 (m-10) REVERT: C 378 LYS cc_start: 0.8291 (mtmt) cc_final: 0.8003 (mtpp) REVERT: C 422 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8208 (m110) REVERT: C 423 TYR cc_start: 0.8206 (t80) cc_final: 0.7883 (t80) REVERT: C 466 ARG cc_start: 0.8068 (ttt-90) cc_final: 0.7740 (ttt-90) REVERT: C 539 VAL cc_start: 0.8668 (p) cc_final: 0.8369 (m) REVERT: C 574 ASP cc_start: 0.8388 (t70) cc_final: 0.7926 (t0) REVERT: C 605 SER cc_start: 0.8490 (p) cc_final: 0.8213 (t) REVERT: C 674 TYR cc_start: 0.8194 (t80) cc_final: 0.7971 (t80) REVERT: C 719 THR cc_start: 0.8502 (t) cc_final: 0.8151 (p) REVERT: C 776 LYS cc_start: 0.8321 (ttpp) cc_final: 0.8103 (ttmm) REVERT: C 808 ASP cc_start: 0.8120 (t0) cc_final: 0.7760 (t0) REVERT: C 868 GLU cc_start: 0.7978 (tp30) cc_final: 0.7627 (tp30) REVERT: C 934 ILE cc_start: 0.8435 (mm) cc_final: 0.8172 (tp) REVERT: C 945 LEU cc_start: 0.8204 (mm) cc_final: 0.7945 (mp) REVERT: C 967 SER cc_start: 0.8819 (t) cc_final: 0.8569 (p) REVERT: C 990 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7914 (mm-30) REVERT: C 1105 THR cc_start: 0.8614 (t) cc_final: 0.8378 (p) REVERT: X 81 MET cc_start: 0.5105 (tmm) cc_final: 0.4392 (tmm) REVERT: X 118 MET cc_start: 0.2920 (tpt) cc_final: 0.2643 (tpt) REVERT: Z 31 CYS cc_start: -0.0541 (OUTLIER) cc_final: -0.1433 (m) REVERT: U 81 MET cc_start: 0.7158 (tpp) cc_final: 0.6630 (tpt) REVERT: V 31 SER cc_start: 0.8324 (m) cc_final: 0.8007 (p) REVERT: R 118 MET cc_start: 0.1440 (tpt) cc_final: 0.0312 (tpt) REVERT: T 43 MET cc_start: -0.4887 (mmm) cc_final: -0.5562 (tmm) REVERT: T 92 MET cc_start: -0.0093 (ptm) cc_final: -0.0444 (tpt) outliers start: 81 outliers final: 47 residues processed: 641 average time/residue: 0.2136 time to fit residues: 229.8067 Evaluate side-chains 595 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 539 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Z residue 31 CYS Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain U residue 52 ILE Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 89 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 460 optimal weight: 0.9980 chunk 451 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 chunk 271 optimal weight: 0.5980 chunk 402 optimal weight: 8.9990 chunk 379 optimal weight: 10.0000 chunk 387 optimal weight: 0.9990 chunk 34 optimal weight: 0.0170 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 762 GLN A 784 GLN A 935 GLN A 955 ASN A1058 HIS B 61 ASN B 519 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 856 ASN B 901 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 658 ASN C 784 GLN C 856 ASN C 955 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.213072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152010 restraints weight = 60509.498| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.73 r_work: 0.3566 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 37090 Z= 0.159 Angle : 0.597 13.124 50680 Z= 0.308 Chirality : 0.046 0.238 5886 Planarity : 0.004 0.049 6480 Dihedral : 5.365 56.833 5866 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.68 % Allowed : 16.30 % Favored : 81.01 % 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: -1.05 (0.12), residues: 4666 helix: 1.76 (0.20), residues: 680 sheet: -0.53 (0.13), residues: 1413 loop : -1.51 (0.11), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 211 TYR 0.027 0.001 TYR B 265 PHE 0.026 0.002 PHE X 64 TRP 0.018 0.001 TRP V 35 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00368 (36997) covalent geometry : angle 0.58496 (50455) SS BOND : bond 0.00578 ( 54) SS BOND : angle 1.88188 ( 108) hydrogen bonds : bond 0.04116 ( 1384) hydrogen bonds : angle 5.78775 ( 3756) link_BETA1-4 : bond 0.00392 ( 2) link_BETA1-4 : angle 1.86805 ( 6) link_NAG-ASN : bond 0.00583 ( 37) link_NAG-ASN : angle 1.95553 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 564 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8797 (mt) cc_final: 0.8558 (mp) REVERT: A 126 VAL cc_start: 0.7527 (p) cc_final: 0.7291 (m) REVERT: A 138 ASP cc_start: 0.7959 (m-30) cc_final: 0.7554 (m-30) REVERT: A 319 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8185 (ptm-80) REVERT: A 452 LEU cc_start: 0.1387 (OUTLIER) cc_final: 0.1125 (pp) REVERT: A 533 LEU cc_start: 0.5698 (tt) cc_final: 0.5485 (tt) REVERT: A 574 ASP cc_start: 0.8140 (m-30) cc_final: 0.7885 (m-30) REVERT: A 602 THR cc_start: 0.8333 (p) cc_final: 0.8033 (m) REVERT: A 745 ASP cc_start: 0.8275 (t0) cc_final: 0.8009 (t0) REVERT: A 975 SER cc_start: 0.8654 (p) cc_final: 0.8334 (t) REVERT: A 1054 GLN cc_start: 0.8237 (mm-40) cc_final: 0.8028 (mm110) REVERT: A 1072 GLU cc_start: 0.8481 (pm20) cc_final: 0.8097 (pm20) REVERT: A 1084 ASP cc_start: 0.8044 (t0) cc_final: 0.7505 (t0) REVERT: A 1094 VAL cc_start: 0.8296 (m) cc_final: 0.8004 (p) REVERT: B 45 SER cc_start: 0.8763 (p) cc_final: 0.8561 (p) REVERT: B 46 SER cc_start: 0.8710 (m) cc_final: 0.8406 (p) REVERT: B 51 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8260 (p) REVERT: B 196 ASN cc_start: 0.7569 (t0) cc_final: 0.7140 (t0) REVERT: B 271 GLN cc_start: 0.8088 (mp10) cc_final: 0.7875 (mt0) REVERT: B 276 LEU cc_start: 0.8499 (tp) cc_final: 0.8198 (tt) REVERT: B 281 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7245 (tm-30) REVERT: B 282 ASN cc_start: 0.8362 (m-40) cc_final: 0.8008 (m-40) REVERT: B 524 VAL cc_start: 0.4667 (OUTLIER) cc_final: 0.4301 (m) REVERT: B 645 THR cc_start: 0.8432 (m) cc_final: 0.8190 (p) REVERT: B 698 SER cc_start: 0.8908 (t) cc_final: 0.8589 (p) REVERT: B 720 ILE cc_start: 0.8643 (mm) cc_final: 0.8368 (mm) REVERT: B 767 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8180 (mt) REVERT: B 855 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.7111 (t80) REVERT: B 900 MET cc_start: 0.8233 (mtt) cc_final: 0.7952 (mtp) REVERT: B 948 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8356 (mp) REVERT: B 967 SER cc_start: 0.8538 (t) cc_final: 0.8338 (t) REVERT: B 973 ILE cc_start: 0.8905 (tt) cc_final: 0.8682 (tt) REVERT: B 983 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7844 (mtm110) REVERT: B 990 GLU cc_start: 0.8101 (tp30) cc_final: 0.7825 (tp30) REVERT: B 998 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8390 (p) REVERT: C 202 LYS cc_start: 0.8082 (mttt) cc_final: 0.7852 (mttp) REVERT: C 269 TYR cc_start: 0.8126 (m-80) cc_final: 0.7811 (m-80) REVERT: C 270 LEU cc_start: 0.8588 (mp) cc_final: 0.8310 (mt) REVERT: C 310 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8529 (ttmt) REVERT: C 317 ASN cc_start: 0.8059 (m-40) cc_final: 0.7734 (m-40) REVERT: C 378 LYS cc_start: 0.8339 (mtmt) cc_final: 0.8076 (mtpp) REVERT: C 428 ASP cc_start: 0.7914 (p0) cc_final: 0.7613 (p0) REVERT: C 466 ARG cc_start: 0.8213 (ttt-90) cc_final: 0.7880 (ttt-90) REVERT: C 509 ARG cc_start: 0.8382 (ttm170) cc_final: 0.7997 (mtt180) REVERT: C 539 VAL cc_start: 0.8678 (p) cc_final: 0.8362 (m) REVERT: C 574 ASP cc_start: 0.8525 (t70) cc_final: 0.8085 (t0) REVERT: C 617 CYS cc_start: 0.7995 (m) cc_final: 0.7752 (m) REVERT: C 670 ILE cc_start: 0.8563 (mm) cc_final: 0.8326 (mt) REVERT: C 719 THR cc_start: 0.8514 (t) cc_final: 0.8187 (p) REVERT: C 775 ASP cc_start: 0.8131 (m-30) cc_final: 0.7903 (m-30) REVERT: C 808 ASP cc_start: 0.8176 (t0) cc_final: 0.7847 (t0) REVERT: C 934 ILE cc_start: 0.8560 (mm) cc_final: 0.8290 (tp) REVERT: C 945 LEU cc_start: 0.8225 (mm) cc_final: 0.7966 (mp) REVERT: C 1105 THR cc_start: 0.8585 (t) cc_final: 0.8379 (p) REVERT: X 81 MET cc_start: 0.4968 (tmm) cc_final: 0.4131 (tmm) REVERT: X 118 MET cc_start: 0.2786 (tpt) cc_final: 0.2472 (tpt) REVERT: U 81 MET cc_start: 0.7289 (tpp) cc_final: 0.6677 (tpt) REVERT: R 118 MET cc_start: 0.1252 (tpt) cc_final: 0.0145 (tpt) REVERT: T 43 MET cc_start: -0.4632 (mmm) cc_final: -0.5489 (tmm) REVERT: T 92 MET cc_start: 0.0042 (ptm) cc_final: -0.0313 (tpt) outliers start: 102 outliers final: 65 residues processed: 636 average time/residue: 0.2053 time to fit residues: 219.3807 Evaluate side-chains 607 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 535 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 291 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 237 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 147 optimal weight: 50.0000 chunk 426 optimal weight: 50.0000 chunk 454 optimal weight: 50.0000 chunk 374 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 220 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN A 762 GLN A 955 ASN A1058 HIS B 81 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B 907 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 751 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 901 GLN C1010 GLN Y 166 GLN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.211525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151612 restraints weight = 60272.499| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.52 r_work: 0.3567 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 37090 Z= 0.191 Angle : 0.609 12.570 50680 Z= 0.314 Chirality : 0.047 0.286 5886 Planarity : 0.005 0.049 6480 Dihedral : 5.228 57.181 5866 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.29 % Allowed : 16.91 % Favored : 79.81 % 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: -0.90 (0.12), residues: 4666 helix: 1.72 (0.20), residues: 677 sheet: -0.30 (0.13), residues: 1430 loop : -1.45 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 190 TYR 0.029 0.002 TYR B 265 PHE 0.025 0.002 PHE C 43 TRP 0.021 0.001 TRP V 35 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00452 (36997) covalent geometry : angle 0.59496 (50455) SS BOND : bond 0.00484 ( 54) SS BOND : angle 2.03280 ( 108) hydrogen bonds : bond 0.04367 ( 1384) hydrogen bonds : angle 5.65346 ( 3756) link_BETA1-4 : bond 0.00497 ( 2) link_BETA1-4 : angle 1.51825 ( 6) link_NAG-ASN : bond 0.00438 ( 37) link_NAG-ASN : angle 2.00724 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 571 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8808 (mt) cc_final: 0.8566 (mp) REVERT: A 52 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 138 ASP cc_start: 0.7938 (m-30) cc_final: 0.7548 (m-30) REVERT: A 269 TYR cc_start: 0.8424 (m-10) cc_final: 0.8082 (m-10) REVERT: A 319 ARG cc_start: 0.8253 (ttp80) cc_final: 0.8037 (ptm-80) REVERT: A 533 LEU cc_start: 0.5941 (tt) cc_final: 0.5729 (tt) REVERT: A 551 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8368 (m) REVERT: A 574 ASP cc_start: 0.8073 (m-30) cc_final: 0.7747 (m-30) REVERT: A 602 THR cc_start: 0.8375 (p) cc_final: 0.8084 (m) REVERT: A 737 ASP cc_start: 0.8240 (t0) cc_final: 0.7912 (t0) REVERT: A 804 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8488 (mm-40) REVERT: A 859 THR cc_start: 0.8538 (m) cc_final: 0.8225 (p) REVERT: A 969 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8497 (mttm) REVERT: A 975 SER cc_start: 0.8716 (p) cc_final: 0.8449 (t) REVERT: A 1010 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8363 (mm-40) REVERT: A 1072 GLU cc_start: 0.8405 (pm20) cc_final: 0.7985 (pm20) REVERT: A 1084 ASP cc_start: 0.7976 (t0) cc_final: 0.7414 (t0) REVERT: B 45 SER cc_start: 0.8736 (p) cc_final: 0.8521 (p) REVERT: B 46 SER cc_start: 0.8734 (m) cc_final: 0.8439 (p) REVERT: B 196 ASN cc_start: 0.7817 (t0) cc_final: 0.7359 (t0) REVERT: B 216 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8036 (mp) REVERT: B 271 GLN cc_start: 0.8106 (mp10) cc_final: 0.7867 (mt0) REVERT: B 276 LEU cc_start: 0.8518 (tp) cc_final: 0.8278 (tt) REVERT: B 281 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7312 (tm-30) REVERT: B 282 ASN cc_start: 0.8317 (m-40) cc_final: 0.7982 (m-40) REVERT: B 524 VAL cc_start: 0.4639 (OUTLIER) cc_final: 0.4282 (m) REVERT: B 698 SER cc_start: 0.8930 (t) cc_final: 0.8616 (p) REVERT: B 710 ASN cc_start: 0.8226 (p0) cc_final: 0.8001 (p0) REVERT: B 735 SER cc_start: 0.8663 (t) cc_final: 0.8285 (m) REVERT: B 900 MET cc_start: 0.8248 (mtt) cc_final: 0.7967 (mtp) REVERT: B 948 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8401 (mp) REVERT: B 973 ILE cc_start: 0.8877 (tt) cc_final: 0.8658 (tt) REVERT: B 983 ARG cc_start: 0.8000 (ttm170) cc_final: 0.7701 (mtm110) REVERT: B 990 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: B 998 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8400 (p) REVERT: B 1091 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7790 (mtt180) REVERT: C 99 ASN cc_start: 0.7953 (t0) cc_final: 0.7669 (p0) REVERT: C 118 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7254 (mt) REVERT: C 270 LEU cc_start: 0.8618 (mp) cc_final: 0.8371 (mt) REVERT: C 290 ASP cc_start: 0.7910 (t0) cc_final: 0.7696 (m-30) REVERT: C 317 ASN cc_start: 0.7971 (m-40) cc_final: 0.7458 (m-40) REVERT: C 383 SER cc_start: 0.8285 (t) cc_final: 0.8030 (m) REVERT: C 420 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7361 (t0) REVERT: C 428 ASP cc_start: 0.7918 (p0) cc_final: 0.7645 (p0) REVERT: C 466 ARG cc_start: 0.8111 (ttt-90) cc_final: 0.7909 (ttt-90) REVERT: C 539 VAL cc_start: 0.8718 (p) cc_final: 0.8395 (m) REVERT: C 574 ASP cc_start: 0.8419 (t70) cc_final: 0.8049 (t0) REVERT: C 617 CYS cc_start: 0.7785 (m) cc_final: 0.7554 (m) REVERT: C 719 THR cc_start: 0.8601 (t) cc_final: 0.8273 (p) REVERT: C 720 ILE cc_start: 0.8448 (pt) cc_final: 0.8132 (mt) REVERT: C 808 ASP cc_start: 0.8083 (t0) cc_final: 0.7794 (t0) REVERT: C 934 ILE cc_start: 0.8658 (mm) cc_final: 0.8351 (tp) REVERT: C 945 LEU cc_start: 0.8253 (mm) cc_final: 0.8007 (mp) REVERT: C 976 VAL cc_start: 0.8678 (p) cc_final: 0.8415 (m) REVERT: C 990 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7910 (tp30) REVERT: C 1017 GLU cc_start: 0.7971 (tp30) cc_final: 0.7248 (tp30) REVERT: C 1092 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7032 (mm-30) REVERT: C 1105 THR cc_start: 0.8647 (t) cc_final: 0.8447 (p) REVERT: X 81 MET cc_start: 0.5295 (tmm) cc_final: 0.4580 (tmm) REVERT: X 118 MET cc_start: 0.2939 (tpt) cc_final: 0.2501 (tpt) REVERT: Y 4 MET cc_start: 0.5955 (pmm) cc_final: 0.3500 (tpt) REVERT: U 81 MET cc_start: 0.7357 (tpp) cc_final: 0.6732 (tpt) REVERT: R 118 MET cc_start: 0.1285 (tpt) cc_final: 0.0206 (tpt) REVERT: T 43 MET cc_start: -0.4520 (mmm) cc_final: -0.5303 (tmm) REVERT: T 92 MET cc_start: 0.0062 (ptm) cc_final: -0.0261 (tpt) outliers start: 125 outliers final: 85 residues processed: 661 average time/residue: 0.1901 time to fit residues: 212.9773 Evaluate side-chains 628 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 535 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 104 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Chi-restraints excluded: chain T residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 66 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 227 optimal weight: 0.5980 chunk 206 optimal weight: 0.9980 chunk 138 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 413 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 135 optimal weight: 50.0000 chunk 236 optimal weight: 0.0170 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 613 GLN A 762 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1054 GLN A1058 HIS B 61 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN C 69 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 777 ASN C 784 GLN C 856 ASN C 913 GLN C1010 GLN V 166 GLN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.212782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152806 restraints weight = 60156.908| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.61 r_work: 0.3590 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37090 Z= 0.124 Angle : 0.565 10.853 50680 Z= 0.291 Chirality : 0.044 0.242 5886 Planarity : 0.004 0.049 6480 Dihedral : 4.885 55.732 5864 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.31 % Allowed : 17.88 % Favored : 78.81 % 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: -0.72 (0.12), residues: 4666 helix: 1.95 (0.20), residues: 671 sheet: -0.17 (0.13), residues: 1431 loop : -1.36 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.022 0.001 TYR C 501 PHE 0.024 0.001 PHE A 592 TRP 0.018 0.001 TRP V 35 HIS 0.003 0.001 HIS S 198 Details of bonding type rmsd covalent geometry : bond 0.00287 (36997) covalent geometry : angle 0.55407 (50455) SS BOND : bond 0.00406 ( 54) SS BOND : angle 1.70232 ( 108) hydrogen bonds : bond 0.03757 ( 1384) hydrogen bonds : angle 5.44998 ( 3756) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.16977 ( 6) link_NAG-ASN : bond 0.00331 ( 37) link_NAG-ASN : angle 1.78828 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 556 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8771 (mt) cc_final: 0.8524 (mp) REVERT: A 138 ASP cc_start: 0.8085 (m-30) cc_final: 0.7685 (m-30) REVERT: A 319 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8118 (ptm-80) REVERT: A 452 LEU cc_start: 0.1171 (OUTLIER) cc_final: 0.0927 (pp) REVERT: A 468 ILE cc_start: 0.2770 (OUTLIER) cc_final: 0.2480 (mm) REVERT: A 574 ASP cc_start: 0.8202 (m-30) cc_final: 0.7886 (m-30) REVERT: A 602 THR cc_start: 0.8330 (p) cc_final: 0.8057 (m) REVERT: A 737 ASP cc_start: 0.8258 (t0) cc_final: 0.7909 (t0) REVERT: A 751 ASN cc_start: 0.8588 (t0) cc_final: 0.8252 (m-40) REVERT: A 821 LEU cc_start: 0.8405 (mt) cc_final: 0.8103 (mp) REVERT: A 859 THR cc_start: 0.8542 (m) cc_final: 0.8237 (p) REVERT: A 969 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8521 (mttm) REVERT: A 975 SER cc_start: 0.8678 (p) cc_final: 0.8393 (t) REVERT: A 976 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8593 (m) REVERT: A 1072 GLU cc_start: 0.8488 (pm20) cc_final: 0.8087 (pm20) REVERT: A 1084 ASP cc_start: 0.8048 (t0) cc_final: 0.7519 (t0) REVERT: A 1094 VAL cc_start: 0.8214 (m) cc_final: 0.7872 (p) REVERT: B 45 SER cc_start: 0.8749 (p) cc_final: 0.8538 (p) REVERT: B 46 SER cc_start: 0.8763 (m) cc_final: 0.8456 (p) REVERT: B 51 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8296 (p) REVERT: B 196 ASN cc_start: 0.7712 (t0) cc_final: 0.7265 (t0) REVERT: B 216 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8026 (mp) REVERT: B 271 GLN cc_start: 0.8122 (mp10) cc_final: 0.7917 (mt0) REVERT: B 276 LEU cc_start: 0.8470 (tp) cc_final: 0.8191 (tt) REVERT: B 281 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7477 (tm-30) REVERT: B 282 ASN cc_start: 0.8336 (m-40) cc_final: 0.8056 (m-40) REVERT: B 524 VAL cc_start: 0.4521 (OUTLIER) cc_final: 0.4155 (m) REVERT: B 698 SER cc_start: 0.8909 (t) cc_final: 0.8610 (p) REVERT: B 710 ASN cc_start: 0.8219 (p0) cc_final: 0.7987 (p0) REVERT: B 735 SER cc_start: 0.8585 (t) cc_final: 0.8192 (m) REVERT: B 791 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7555 (p) REVERT: B 882 ILE cc_start: 0.8562 (pt) cc_final: 0.8282 (mt) REVERT: B 900 MET cc_start: 0.8236 (mtt) cc_final: 0.7944 (mtp) REVERT: B 948 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B 973 ILE cc_start: 0.8877 (tt) cc_final: 0.8596 (tt) REVERT: B 983 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7841 (mtm110) REVERT: B 990 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: C 28 TYR cc_start: 0.7407 (m-10) cc_final: 0.7190 (m-10) REVERT: C 99 ASN cc_start: 0.8028 (t0) cc_final: 0.7688 (p0) REVERT: C 118 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7304 (mt) REVERT: C 270 LEU cc_start: 0.8581 (mp) cc_final: 0.8333 (mt) REVERT: C 317 ASN cc_start: 0.8010 (m-40) cc_final: 0.7570 (m-40) REVERT: C 364 ASP cc_start: 0.8314 (t70) cc_final: 0.7954 (t0) REVERT: C 383 SER cc_start: 0.8198 (t) cc_final: 0.7904 (m) REVERT: C 423 TYR cc_start: 0.8203 (t80) cc_final: 0.7698 (t80) REVERT: C 428 ASP cc_start: 0.8071 (p0) cc_final: 0.7792 (p0) REVERT: C 539 VAL cc_start: 0.8644 (p) cc_final: 0.8328 (m) REVERT: C 560 LEU cc_start: 0.8605 (mm) cc_final: 0.8392 (mp) REVERT: C 574 ASP cc_start: 0.8483 (t70) cc_final: 0.8107 (t0) REVERT: C 719 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8200 (p) REVERT: C 720 ILE cc_start: 0.8391 (pt) cc_final: 0.8094 (mt) REVERT: C 808 ASP cc_start: 0.8125 (t0) cc_final: 0.7810 (t0) REVERT: C 934 ILE cc_start: 0.8590 (mm) cc_final: 0.8287 (tp) REVERT: C 945 LEU cc_start: 0.8181 (mm) cc_final: 0.7924 (mp) REVERT: C 976 VAL cc_start: 0.8645 (p) cc_final: 0.8384 (m) REVERT: C 1092 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7206 (mm-30) REVERT: X 81 MET cc_start: 0.5350 (tmm) cc_final: 0.4660 (tmm) REVERT: X 118 MET cc_start: 0.2971 (tpt) cc_final: 0.2521 (tpt) REVERT: Y 4 MET cc_start: 0.5987 (pmm) cc_final: 0.3455 (ttp) REVERT: U 81 MET cc_start: 0.7405 (tpp) cc_final: 0.6716 (tpt) REVERT: R 118 MET cc_start: 0.1370 (tpt) cc_final: 0.0330 (tpt) REVERT: T 43 MET cc_start: -0.4480 (mmm) cc_final: -0.5280 (tmm) REVERT: T 92 MET cc_start: 0.0100 (ptm) cc_final: -0.0207 (tpt) outliers start: 126 outliers final: 90 residues processed: 650 average time/residue: 0.1932 time to fit residues: 213.1274 Evaluate side-chains 636 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 535 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 31 CYS Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 166 GLN Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 183 LYS Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 66 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 283 optimal weight: 0.9990 chunk 281 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 371 optimal weight: 2.9990 chunk 138 optimal weight: 50.0000 chunk 409 optimal weight: 9.9990 chunk 198 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 317 ASN A 613 GLN A 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 61 ASN B 907 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 935 GLN U 59 ASN ** V 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.212175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151456 restraints weight = 60154.887| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.65 r_work: 0.3599 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37090 Z= 0.159 Angle : 0.581 11.904 50680 Z= 0.298 Chirality : 0.045 0.227 5886 Planarity : 0.004 0.052 6480 Dihedral : 4.848 56.026 5864 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.58 % Allowed : 18.33 % Favored : 78.10 % 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: -0.67 (0.12), residues: 4666 helix: 1.88 (0.20), residues: 674 sheet: -0.13 (0.13), residues: 1424 loop : -1.30 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 47 TYR 0.026 0.001 TYR B 265 PHE 0.020 0.002 PHE A 592 TRP 0.020 0.001 TRP V 35 HIS 0.017 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00377 (36997) covalent geometry : angle 0.56909 (50455) SS BOND : bond 0.00474 ( 54) SS BOND : angle 1.96791 ( 108) hydrogen bonds : bond 0.03935 ( 1384) hydrogen bonds : angle 5.40733 ( 3756) link_BETA1-4 : bond 0.00258 ( 2) link_BETA1-4 : angle 1.13015 ( 6) link_NAG-ASN : bond 0.00367 ( 37) link_NAG-ASN : angle 1.82163 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 533 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8794 (mt) cc_final: 0.8551 (mp) REVERT: A 138 ASP cc_start: 0.8109 (m-30) cc_final: 0.7694 (m-30) REVERT: A 281 GLU cc_start: 0.8409 (pt0) cc_final: 0.8042 (pp20) REVERT: A 319 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8176 (ptm-80) REVERT: A 452 LEU cc_start: 0.1206 (OUTLIER) cc_final: 0.0973 (pp) REVERT: A 468 ILE cc_start: 0.2804 (OUTLIER) cc_final: 0.2517 (mm) REVERT: A 574 ASP cc_start: 0.8223 (m-30) cc_final: 0.7912 (m-30) REVERT: A 602 THR cc_start: 0.8364 (p) cc_final: 0.8084 (m) REVERT: A 745 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.8041 (t70) REVERT: A 751 ASN cc_start: 0.8641 (t0) cc_final: 0.8307 (m-40) REVERT: A 859 THR cc_start: 0.8567 (m) cc_final: 0.8263 (p) REVERT: A 975 SER cc_start: 0.8670 (p) cc_final: 0.8368 (t) REVERT: A 976 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8566 (m) REVERT: A 1029 MET cc_start: 0.8285 (tpp) cc_final: 0.7851 (ttp) REVERT: A 1072 GLU cc_start: 0.8504 (pm20) cc_final: 0.8188 (pm20) REVERT: A 1084 ASP cc_start: 0.8118 (t0) cc_final: 0.7592 (t0) REVERT: B 45 SER cc_start: 0.8736 (p) cc_final: 0.8525 (p) REVERT: B 46 SER cc_start: 0.8774 (m) cc_final: 0.8481 (p) REVERT: B 196 ASN cc_start: 0.7788 (t0) cc_final: 0.7318 (t0) REVERT: B 216 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 239 GLN cc_start: 0.7755 (mt0) cc_final: 0.7502 (mt0) REVERT: B 276 LEU cc_start: 0.8487 (tp) cc_final: 0.8246 (tt) REVERT: B 281 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7514 (tm-30) REVERT: B 282 ASN cc_start: 0.8370 (m-40) cc_final: 0.8049 (m-40) REVERT: B 524 VAL cc_start: 0.4427 (OUTLIER) cc_final: 0.4117 (m) REVERT: B 698 SER cc_start: 0.8934 (t) cc_final: 0.8629 (p) REVERT: B 710 ASN cc_start: 0.8273 (p0) cc_final: 0.8026 (p0) REVERT: B 735 SER cc_start: 0.8684 (t) cc_final: 0.8271 (m) REVERT: B 791 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7612 (p) REVERT: B 882 ILE cc_start: 0.8579 (pt) cc_final: 0.8302 (mt) REVERT: B 900 MET cc_start: 0.8219 (mtt) cc_final: 0.7926 (mtp) REVERT: B 948 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8393 (mp) REVERT: B 973 ILE cc_start: 0.8876 (tt) cc_final: 0.8568 (tt) REVERT: B 983 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7852 (mtm110) REVERT: B 1031 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7326 (mt-10) REVERT: B 1084 ASP cc_start: 0.8200 (t0) cc_final: 0.7845 (t0) REVERT: C 99 ASN cc_start: 0.8038 (t0) cc_final: 0.7675 (p0) REVERT: C 118 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7332 (mt) REVERT: C 270 LEU cc_start: 0.8584 (mp) cc_final: 0.8333 (mt) REVERT: C 317 ASN cc_start: 0.8067 (m-40) cc_final: 0.7773 (m-40) REVERT: C 383 SER cc_start: 0.8230 (t) cc_final: 0.7952 (m) REVERT: C 420 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7389 (t0) REVERT: C 423 TYR cc_start: 0.8210 (t80) cc_final: 0.7692 (t80) REVERT: C 428 ASP cc_start: 0.8149 (p0) cc_final: 0.7873 (p0) REVERT: C 539 VAL cc_start: 0.8662 (p) cc_final: 0.8351 (m) REVERT: C 560 LEU cc_start: 0.8588 (mm) cc_final: 0.8378 (mp) REVERT: C 574 ASP cc_start: 0.8502 (t70) cc_final: 0.8124 (t0) REVERT: C 719 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8218 (p) REVERT: C 720 ILE cc_start: 0.8409 (pt) cc_final: 0.8153 (mt) REVERT: C 808 ASP cc_start: 0.8126 (t0) cc_final: 0.7768 (t0) REVERT: C 934 ILE cc_start: 0.8578 (mm) cc_final: 0.8269 (tp) REVERT: C 945 LEU cc_start: 0.8218 (mm) cc_final: 0.7969 (mp) REVERT: C 976 VAL cc_start: 0.8633 (p) cc_final: 0.8358 (m) REVERT: C 990 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8013 (tp30) REVERT: C 1092 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7299 (mm-30) REVERT: X 81 MET cc_start: 0.5477 (tmm) cc_final: 0.4715 (tmm) REVERT: X 118 MET cc_start: 0.2898 (tpt) cc_final: 0.2450 (tpt) REVERT: Z 15 GLU cc_start: 0.4202 (OUTLIER) cc_final: 0.3895 (mm-30) REVERT: U 81 MET cc_start: 0.7360 (tpp) cc_final: 0.6633 (tpt) REVERT: R 118 MET cc_start: 0.1217 (tpt) cc_final: 0.0197 (tpt) REVERT: T 43 MET cc_start: -0.4388 (mmm) cc_final: -0.5264 (tmm) REVERT: T 92 MET cc_start: 0.0231 (ptm) cc_final: -0.0135 (tpt) outliers start: 136 outliers final: 100 residues processed: 627 average time/residue: 0.1926 time to fit residues: 203.9173 Evaluate side-chains 636 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 524 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 31 CYS Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 59 ASN Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 194 CYS Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 406 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 chunk 437 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 152 optimal weight: 0.0270 chunk 200 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 272 optimal weight: 0.8980 chunk 19 optimal weight: 0.0030 overall best weight: 0.5248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 505 HIS C 196 ASN C 658 ASN C 784 GLN C 856 ASN C 913 GLN C 935 GLN V 166 GLN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 GLN S 199 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.212728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153040 restraints weight = 60472.945| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.54 r_work: 0.3584 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37090 Z= 0.130 Angle : 0.568 11.025 50680 Z= 0.290 Chirality : 0.044 0.231 5886 Planarity : 0.004 0.056 6480 Dihedral : 4.738 54.728 5864 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.63 % Allowed : 18.51 % Favored : 77.86 % 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: -0.59 (0.12), residues: 4666 helix: 1.94 (0.20), residues: 682 sheet: -0.05 (0.13), residues: 1431 loop : -1.28 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 466 TYR 0.025 0.001 TYR C 501 PHE 0.024 0.001 PHE C 43 TRP 0.020 0.001 TRP V 35 HIS 0.004 0.001 HIS S 198 Details of bonding type rmsd covalent geometry : bond 0.00305 (36997) covalent geometry : angle 0.55586 (50455) SS BOND : bond 0.00445 ( 54) SS BOND : angle 1.91557 ( 108) hydrogen bonds : bond 0.03725 ( 1384) hydrogen bonds : angle 5.31866 ( 3756) link_BETA1-4 : bond 0.00336 ( 2) link_BETA1-4 : angle 1.06519 ( 6) link_NAG-ASN : bond 0.00335 ( 37) link_NAG-ASN : angle 1.75574 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 521 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8780 (mt) cc_final: 0.8541 (mp) REVERT: A 138 ASP cc_start: 0.8074 (m-30) cc_final: 0.7565 (m-30) REVERT: A 319 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8139 (ptm-80) REVERT: A 452 LEU cc_start: 0.1216 (OUTLIER) cc_final: 0.0979 (pp) REVERT: A 468 ILE cc_start: 0.2779 (OUTLIER) cc_final: 0.2483 (mm) REVERT: A 602 THR cc_start: 0.8348 (p) cc_final: 0.8067 (m) REVERT: A 745 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7978 (t70) REVERT: A 751 ASN cc_start: 0.8575 (t0) cc_final: 0.8251 (m-40) REVERT: A 821 LEU cc_start: 0.8371 (mt) cc_final: 0.8073 (mp) REVERT: A 859 THR cc_start: 0.8557 (m) cc_final: 0.8264 (p) REVERT: A 975 SER cc_start: 0.8703 (p) cc_final: 0.8401 (t) REVERT: A 976 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8533 (m) REVERT: A 1029 MET cc_start: 0.8271 (tpp) cc_final: 0.7724 (ttp) REVERT: A 1072 GLU cc_start: 0.8459 (pm20) cc_final: 0.8152 (pm20) REVERT: A 1084 ASP cc_start: 0.8095 (t0) cc_final: 0.7572 (t0) REVERT: B 45 SER cc_start: 0.8724 (p) cc_final: 0.8508 (p) REVERT: B 46 SER cc_start: 0.8778 (m) cc_final: 0.8485 (p) REVERT: B 196 ASN cc_start: 0.7708 (t0) cc_final: 0.7251 (t0) REVERT: B 216 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8009 (mp) REVERT: B 271 GLN cc_start: 0.8249 (mt0) cc_final: 0.7898 (mt0) REVERT: B 276 LEU cc_start: 0.8469 (tp) cc_final: 0.8222 (tt) REVERT: B 281 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 282 ASN cc_start: 0.8339 (m-40) cc_final: 0.8022 (m-40) REVERT: B 524 VAL cc_start: 0.4210 (OUTLIER) cc_final: 0.3872 (m) REVERT: B 698 SER cc_start: 0.8926 (t) cc_final: 0.8619 (p) REVERT: B 710 ASN cc_start: 0.8294 (p0) cc_final: 0.8030 (p0) REVERT: B 735 SER cc_start: 0.8631 (t) cc_final: 0.8216 (m) REVERT: B 791 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7641 (p) REVERT: B 882 ILE cc_start: 0.8529 (pt) cc_final: 0.8306 (mt) REVERT: B 900 MET cc_start: 0.8190 (mtt) cc_final: 0.7906 (mtp) REVERT: B 948 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8351 (mp) REVERT: B 973 ILE cc_start: 0.8866 (tt) cc_final: 0.8570 (tt) REVERT: B 983 ARG cc_start: 0.8238 (ttm170) cc_final: 0.7844 (mtm110) REVERT: B 998 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8351 (p) REVERT: B 1084 ASP cc_start: 0.8138 (t0) cc_final: 0.7781 (t0) REVERT: C 43 PHE cc_start: 0.8627 (t80) cc_final: 0.8398 (t80) REVERT: C 99 ASN cc_start: 0.8023 (t0) cc_final: 0.7632 (p0) REVERT: C 118 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7298 (mt) REVERT: C 270 LEU cc_start: 0.8576 (mp) cc_final: 0.8323 (mt) REVERT: C 317 ASN cc_start: 0.8046 (m-40) cc_final: 0.7752 (m-40) REVERT: C 383 SER cc_start: 0.8179 (t) cc_final: 0.7877 (m) REVERT: C 420 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7328 (t0) REVERT: C 423 TYR cc_start: 0.8129 (t80) cc_final: 0.7900 (t80) REVERT: C 428 ASP cc_start: 0.8137 (p0) cc_final: 0.7847 (p0) REVERT: C 539 VAL cc_start: 0.8641 (p) cc_final: 0.8314 (m) REVERT: C 574 ASP cc_start: 0.8456 (t70) cc_final: 0.8054 (t0) REVERT: C 719 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8199 (p) REVERT: C 720 ILE cc_start: 0.8380 (pt) cc_final: 0.8118 (mt) REVERT: C 808 ASP cc_start: 0.8081 (t0) cc_final: 0.7741 (t0) REVERT: C 934 ILE cc_start: 0.8569 (mm) cc_final: 0.8259 (tp) REVERT: C 945 LEU cc_start: 0.8178 (mm) cc_final: 0.7931 (mp) REVERT: C 976 VAL cc_start: 0.8637 (p) cc_final: 0.8387 (m) REVERT: C 990 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7917 (tp30) REVERT: C 1017 GLU cc_start: 0.8201 (tp30) cc_final: 0.7615 (tp30) REVERT: C 1092 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7281 (mm-30) REVERT: X 81 MET cc_start: 0.5455 (tmm) cc_final: 0.4726 (tmm) REVERT: X 118 MET cc_start: 0.3031 (tpt) cc_final: 0.2663 (tpt) REVERT: Z 15 GLU cc_start: 0.4274 (OUTLIER) cc_final: 0.3991 (mm-30) REVERT: R 118 MET cc_start: 0.1357 (tpt) cc_final: 0.0345 (tpt) REVERT: T 43 MET cc_start: -0.4427 (mmm) cc_final: -0.5285 (tmm) REVERT: T 92 MET cc_start: 0.0041 (ptm) cc_final: -0.0218 (tpt) outliers start: 138 outliers final: 112 residues processed: 623 average time/residue: 0.2036 time to fit residues: 214.9624 Evaluate side-chains 631 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 506 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 31 CYS Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 166 GLN Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 194 CYS Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 299 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 251 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 762 GLN A 955 ASN B 207 HIS C 69 HIS C 658 ASN C 784 GLN C 913 GLN C 935 GLN C1005 GLN U 59 ASN V 166 GLN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 HIS S 199 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.211653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151903 restraints weight = 59841.212| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.52 r_work: 0.3561 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37090 Z= 0.187 Angle : 0.593 11.769 50680 Z= 0.304 Chirality : 0.046 0.210 5886 Planarity : 0.005 0.058 6480 Dihedral : 4.818 55.696 5864 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.84 % Allowed : 18.96 % Favored : 77.20 % 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: -0.63 (0.12), residues: 4666 helix: 1.76 (0.20), residues: 686 sheet: -0.05 (0.13), residues: 1446 loop : -1.28 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 466 TYR 0.029 0.001 TYR B 265 PHE 0.025 0.002 PHE B 201 TRP 0.019 0.001 TRP V 35 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00445 (36997) covalent geometry : angle 0.58031 (50455) SS BOND : bond 0.00458 ( 54) SS BOND : angle 2.04511 ( 108) hydrogen bonds : bond 0.04113 ( 1384) hydrogen bonds : angle 5.35415 ( 3756) link_BETA1-4 : bond 0.00404 ( 2) link_BETA1-4 : angle 1.09980 ( 6) link_NAG-ASN : bond 0.00377 ( 37) link_NAG-ASN : angle 1.83481 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 520 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8792 (mt) cc_final: 0.8544 (mp) REVERT: A 138 ASP cc_start: 0.8101 (m-30) cc_final: 0.7602 (m-30) REVERT: A 269 TYR cc_start: 0.8448 (m-10) cc_final: 0.8136 (m-10) REVERT: A 281 GLU cc_start: 0.8336 (pt0) cc_final: 0.7991 (pp20) REVERT: A 319 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8172 (ptm-80) REVERT: A 452 LEU cc_start: 0.1343 (OUTLIER) cc_final: 0.1109 (pp) REVERT: A 468 ILE cc_start: 0.2778 (OUTLIER) cc_final: 0.2478 (mm) REVERT: A 551 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8313 (m) REVERT: A 578 ASP cc_start: 0.8165 (t0) cc_final: 0.7943 (t70) REVERT: A 602 THR cc_start: 0.8379 (p) cc_final: 0.8081 (m) REVERT: A 751 ASN cc_start: 0.8648 (t0) cc_final: 0.8311 (m-40) REVERT: A 859 THR cc_start: 0.8593 (m) cc_final: 0.8311 (p) REVERT: A 975 SER cc_start: 0.8676 (p) cc_final: 0.8391 (t) REVERT: A 976 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8570 (m) REVERT: A 1029 MET cc_start: 0.8375 (tpp) cc_final: 0.7628 (ttp) REVERT: A 1072 GLU cc_start: 0.8507 (pm20) cc_final: 0.8231 (pm20) REVERT: A 1084 ASP cc_start: 0.8160 (t0) cc_final: 0.7652 (t0) REVERT: B 45 SER cc_start: 0.8766 (p) cc_final: 0.8551 (p) REVERT: B 46 SER cc_start: 0.8805 (m) cc_final: 0.8520 (p) REVERT: B 191 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 196 ASN cc_start: 0.7843 (t0) cc_final: 0.7404 (t0) REVERT: B 239 GLN cc_start: 0.7791 (mt0) cc_final: 0.7539 (tt0) REVERT: B 271 GLN cc_start: 0.8302 (mt0) cc_final: 0.7947 (mt0) REVERT: B 276 LEU cc_start: 0.8484 (tp) cc_final: 0.8246 (tt) REVERT: B 281 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7553 (tm-30) REVERT: B 282 ASN cc_start: 0.8367 (m-40) cc_final: 0.8041 (m-40) REVERT: B 524 VAL cc_start: 0.4140 (OUTLIER) cc_final: 0.3787 (m) REVERT: B 698 SER cc_start: 0.8949 (t) cc_final: 0.8655 (p) REVERT: B 710 ASN cc_start: 0.8374 (p0) cc_final: 0.8090 (p0) REVERT: B 791 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 900 MET cc_start: 0.8224 (mtt) cc_final: 0.7935 (mtp) REVERT: B 948 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8407 (mp) REVERT: B 973 ILE cc_start: 0.8880 (tt) cc_final: 0.8618 (tt) REVERT: B 983 ARG cc_start: 0.8311 (ttm170) cc_final: 0.7916 (mtm110) REVERT: B 990 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: B 998 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8388 (p) REVERT: B 1084 ASP cc_start: 0.8201 (t0) cc_final: 0.7850 (t0) REVERT: C 99 ASN cc_start: 0.8071 (t0) cc_final: 0.7641 (p0) REVERT: C 118 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7340 (mt) REVERT: C 270 LEU cc_start: 0.8586 (mp) cc_final: 0.8328 (mt) REVERT: C 317 ASN cc_start: 0.8068 (m-40) cc_final: 0.7769 (m-40) REVERT: C 383 SER cc_start: 0.8250 (t) cc_final: 0.7985 (m) REVERT: C 420 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7364 (t0) REVERT: C 423 TYR cc_start: 0.8249 (t80) cc_final: 0.8007 (t80) REVERT: C 428 ASP cc_start: 0.8166 (p0) cc_final: 0.7873 (p0) REVERT: C 498 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7525 (mmt90) REVERT: C 539 VAL cc_start: 0.8688 (p) cc_final: 0.8363 (m) REVERT: C 574 ASP cc_start: 0.8570 (t70) cc_final: 0.8206 (t0) REVERT: C 719 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8249 (p) REVERT: C 720 ILE cc_start: 0.8401 (pt) cc_final: 0.8161 (mt) REVERT: C 808 ASP cc_start: 0.8112 (t0) cc_final: 0.7768 (t0) REVERT: C 934 ILE cc_start: 0.8587 (mm) cc_final: 0.8283 (tp) REVERT: C 945 LEU cc_start: 0.8249 (mm) cc_final: 0.8006 (mp) REVERT: C 976 VAL cc_start: 0.8642 (p) cc_final: 0.8393 (m) REVERT: C 990 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7996 (tp30) REVERT: C 1092 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7343 (mm-30) REVERT: X 81 MET cc_start: 0.5462 (tmm) cc_final: 0.4739 (tmm) REVERT: X 118 MET cc_start: 0.3067 (tpt) cc_final: 0.2692 (tpt) REVERT: Z 15 GLU cc_start: 0.4403 (OUTLIER) cc_final: 0.4130 (mm-30) REVERT: U 81 MET cc_start: 0.7065 (tpt) cc_final: 0.6695 (tpt) REVERT: V 147 GLN cc_start: 0.3130 (OUTLIER) cc_final: 0.2015 (tm-30) REVERT: V 172 THR cc_start: 0.5177 (p) cc_final: 0.4509 (t) REVERT: R 118 MET cc_start: 0.1372 (tpt) cc_final: 0.0363 (tpt) REVERT: T 43 MET cc_start: -0.4411 (mmm) cc_final: -0.5326 (tmm) outliers start: 146 outliers final: 113 residues processed: 619 average time/residue: 0.1990 time to fit residues: 209.3243 Evaluate side-chains 646 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 518 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 194 CYS Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 219 optimal weight: 0.9980 chunk 260 optimal weight: 0.7980 chunk 240 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 370 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 458 optimal weight: 0.9980 chunk 340 optimal weight: 9.9990 chunk 130 optimal weight: 40.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 762 GLN A 955 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 239 GLN C 658 ASN C 784 GLN C 856 ASN C 913 GLN C 935 GLN C1010 GLN U 59 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.211960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152612 restraints weight = 60230.894| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.52 r_work: 0.3566 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37090 Z= 0.162 Angle : 0.592 11.554 50680 Z= 0.302 Chirality : 0.045 0.269 5886 Planarity : 0.004 0.059 6480 Dihedral : 4.780 55.283 5864 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.55 % Allowed : 19.20 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.12), residues: 4666 helix: 1.91 (0.20), residues: 672 sheet: 0.01 (0.13), residues: 1414 loop : -1.28 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 466 TYR 0.026 0.001 TYR B 265 PHE 0.035 0.002 PHE B 643 TRP 0.019 0.001 TRP V 35 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00383 (36997) covalent geometry : angle 0.57746 (50455) SS BOND : bond 0.00455 ( 54) SS BOND : angle 2.19719 ( 108) hydrogen bonds : bond 0.03968 ( 1384) hydrogen bonds : angle 5.30826 ( 3756) link_BETA1-4 : bond 0.00336 ( 2) link_BETA1-4 : angle 1.03168 ( 6) link_NAG-ASN : bond 0.00384 ( 37) link_NAG-ASN : angle 1.84851 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 526 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8768 (mt) cc_final: 0.8525 (mp) REVERT: A 138 ASP cc_start: 0.8057 (m-30) cc_final: 0.7570 (m-30) REVERT: A 269 TYR cc_start: 0.8417 (m-10) cc_final: 0.8123 (m-10) REVERT: A 319 ARG cc_start: 0.8366 (ttp80) cc_final: 0.8072 (ptm-80) REVERT: A 452 LEU cc_start: 0.1337 (OUTLIER) cc_final: 0.1100 (pp) REVERT: A 551 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8298 (m) REVERT: A 578 ASP cc_start: 0.8099 (t0) cc_final: 0.7864 (t70) REVERT: A 602 THR cc_start: 0.8272 (p) cc_final: 0.8056 (m) REVERT: A 751 ASN cc_start: 0.8613 (t0) cc_final: 0.8294 (m-40) REVERT: A 821 LEU cc_start: 0.8404 (mt) cc_final: 0.8094 (mp) REVERT: A 859 THR cc_start: 0.8570 (m) cc_final: 0.8296 (p) REVERT: A 975 SER cc_start: 0.8659 (p) cc_final: 0.8400 (t) REVERT: A 976 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8533 (m) REVERT: A 1029 MET cc_start: 0.8353 (tpp) cc_final: 0.7621 (ttp) REVERT: A 1084 ASP cc_start: 0.8099 (t0) cc_final: 0.7587 (t0) REVERT: B 45 SER cc_start: 0.8778 (p) cc_final: 0.8563 (p) REVERT: B 46 SER cc_start: 0.8810 (m) cc_final: 0.8524 (p) REVERT: B 191 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7904 (mt-10) REVERT: B 196 ASN cc_start: 0.7779 (t0) cc_final: 0.7335 (t0) REVERT: B 239 GLN cc_start: 0.7742 (mt0) cc_final: 0.7497 (tt0) REVERT: B 276 LEU cc_start: 0.8487 (tp) cc_final: 0.8248 (tt) REVERT: B 281 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7523 (tm-30) REVERT: B 282 ASN cc_start: 0.8308 (m-40) cc_final: 0.7997 (m-40) REVERT: B 524 VAL cc_start: 0.3970 (OUTLIER) cc_final: 0.3607 (m) REVERT: B 698 SER cc_start: 0.8940 (t) cc_final: 0.8650 (p) REVERT: B 710 ASN cc_start: 0.8394 (p0) cc_final: 0.8088 (p0) REVERT: B 720 ILE cc_start: 0.8537 (mm) cc_final: 0.8201 (mm) REVERT: B 791 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7777 (p) REVERT: B 900 MET cc_start: 0.8211 (mtt) cc_final: 0.7934 (mtp) REVERT: B 948 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8373 (mp) REVERT: B 973 ILE cc_start: 0.8869 (tt) cc_final: 0.8600 (tt) REVERT: B 983 ARG cc_start: 0.8218 (ttm170) cc_final: 0.7812 (mtm110) REVERT: B 990 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: B 998 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8369 (p) REVERT: B 1084 ASP cc_start: 0.8149 (t0) cc_final: 0.7803 (t0) REVERT: C 81 ASN cc_start: 0.6161 (OUTLIER) cc_final: 0.5702 (t0) REVERT: C 99 ASN cc_start: 0.8053 (t0) cc_final: 0.7634 (p0) REVERT: C 118 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7314 (mt) REVERT: C 270 LEU cc_start: 0.8582 (mp) cc_final: 0.8329 (mt) REVERT: C 317 ASN cc_start: 0.8024 (m-40) cc_final: 0.7737 (m-40) REVERT: C 364 ASP cc_start: 0.8288 (t70) cc_final: 0.7859 (t0) REVERT: C 383 SER cc_start: 0.8224 (t) cc_final: 0.7943 (m) REVERT: C 420 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7305 (t0) REVERT: C 423 TYR cc_start: 0.8201 (t80) cc_final: 0.7972 (t80) REVERT: C 428 ASP cc_start: 0.8135 (p0) cc_final: 0.7845 (p0) REVERT: C 539 VAL cc_start: 0.8671 (p) cc_final: 0.8351 (m) REVERT: C 574 ASP cc_start: 0.8565 (t70) cc_final: 0.8212 (t0) REVERT: C 719 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8230 (p) REVERT: C 720 ILE cc_start: 0.8399 (pt) cc_final: 0.8144 (mt) REVERT: C 808 ASP cc_start: 0.8093 (t0) cc_final: 0.7768 (t0) REVERT: C 934 ILE cc_start: 0.8614 (mm) cc_final: 0.8304 (tp) REVERT: C 945 LEU cc_start: 0.8224 (mm) cc_final: 0.7982 (mp) REVERT: C 976 VAL cc_start: 0.8637 (p) cc_final: 0.8390 (m) REVERT: C 990 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7925 (tp30) REVERT: X 81 MET cc_start: 0.5484 (tmm) cc_final: 0.4762 (tmm) REVERT: X 118 MET cc_start: 0.3029 (tpt) cc_final: 0.2663 (tpt) REVERT: Y 4 MET cc_start: 0.5907 (pmm) cc_final: 0.3591 (tpt) REVERT: Z 15 GLU cc_start: 0.4408 (OUTLIER) cc_final: 0.4144 (mm-30) REVERT: U 81 MET cc_start: 0.7099 (tpt) cc_final: 0.6700 (tpt) REVERT: V 147 GLN cc_start: 0.3061 (OUTLIER) cc_final: 0.1958 (tm-30) REVERT: R 118 MET cc_start: 0.1309 (tpt) cc_final: 0.0316 (tpt) REVERT: T 43 MET cc_start: -0.4311 (mmm) cc_final: -0.5291 (tmm) outliers start: 135 outliers final: 112 residues processed: 621 average time/residue: 0.1878 time to fit residues: 199.1740 Evaluate side-chains 640 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 514 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 194 CYS Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 138 optimal weight: 50.0000 chunk 31 optimal weight: 7.9990 chunk 372 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 262 optimal weight: 0.0010 chunk 298 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 762 GLN A 955 ASN B 755 GLN B1135 ASN C 69 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 784 GLN C 913 GLN C 935 GLN C1005 GLN X 6 GLN U 59 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 199 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.211915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152458 restraints weight = 60005.713| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.51 r_work: 0.3570 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37090 Z= 0.152 Angle : 0.591 12.626 50680 Z= 0.302 Chirality : 0.045 0.262 5886 Planarity : 0.004 0.060 6480 Dihedral : 4.754 55.303 5864 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.42 % Allowed : 19.56 % Favored : 77.02 % 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: -0.54 (0.12), residues: 4666 helix: 1.94 (0.20), residues: 672 sheet: 0.03 (0.13), residues: 1418 loop : -1.25 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 466 TYR 0.025 0.001 TYR B 265 PHE 0.053 0.002 PHE B 643 TRP 0.019 0.001 TRP V 35 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00361 (36997) covalent geometry : angle 0.57687 (50455) SS BOND : bond 0.00457 ( 54) SS BOND : angle 2.20820 ( 108) hydrogen bonds : bond 0.03914 ( 1384) hydrogen bonds : angle 5.27079 ( 3756) link_BETA1-4 : bond 0.00352 ( 2) link_BETA1-4 : angle 1.07369 ( 6) link_NAG-ASN : bond 0.00327 ( 37) link_NAG-ASN : angle 1.80686 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 520 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8791 (mt) cc_final: 0.8558 (mp) REVERT: A 138 ASP cc_start: 0.7956 (m-30) cc_final: 0.7559 (m-30) REVERT: A 269 TYR cc_start: 0.8403 (m-10) cc_final: 0.8096 (m-10) REVERT: A 281 GLU cc_start: 0.8127 (pt0) cc_final: 0.7863 (pp20) REVERT: A 319 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7883 (ptm-80) REVERT: A 452 LEU cc_start: 0.1263 (OUTLIER) cc_final: 0.1035 (pp) REVERT: A 468 ILE cc_start: 0.2764 (OUTLIER) cc_final: 0.2466 (mm) REVERT: A 551 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8305 (m) REVERT: A 751 ASN cc_start: 0.8535 (t0) cc_final: 0.8210 (m-40) REVERT: A 821 LEU cc_start: 0.8395 (mt) cc_final: 0.8079 (mp) REVERT: A 859 THR cc_start: 0.8583 (m) cc_final: 0.8304 (p) REVERT: A 975 SER cc_start: 0.8719 (p) cc_final: 0.8442 (t) REVERT: A 976 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8549 (m) REVERT: A 1029 MET cc_start: 0.8373 (tpp) cc_final: 0.7655 (ttp) REVERT: A 1084 ASP cc_start: 0.8000 (t0) cc_final: 0.7465 (t0) REVERT: B 45 SER cc_start: 0.8739 (p) cc_final: 0.8519 (p) REVERT: B 46 SER cc_start: 0.8795 (m) cc_final: 0.8506 (p) REVERT: B 196 ASN cc_start: 0.7771 (t0) cc_final: 0.7330 (t0) REVERT: B 239 GLN cc_start: 0.7671 (mt0) cc_final: 0.7404 (tt0) REVERT: B 276 LEU cc_start: 0.8502 (tp) cc_final: 0.8259 (tt) REVERT: B 281 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 282 ASN cc_start: 0.8238 (m-40) cc_final: 0.7926 (m-40) REVERT: B 524 VAL cc_start: 0.3822 (OUTLIER) cc_final: 0.3454 (m) REVERT: B 698 SER cc_start: 0.8937 (t) cc_final: 0.8640 (p) REVERT: B 710 ASN cc_start: 0.8432 (p0) cc_final: 0.8129 (p0) REVERT: B 720 ILE cc_start: 0.8567 (mm) cc_final: 0.8230 (mm) REVERT: B 791 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7783 (p) REVERT: B 900 MET cc_start: 0.8234 (mtt) cc_final: 0.7956 (mtp) REVERT: B 948 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8359 (mp) REVERT: B 973 ILE cc_start: 0.8847 (tt) cc_final: 0.8561 (tt) REVERT: B 983 ARG cc_start: 0.7991 (ttm170) cc_final: 0.7630 (mtm110) REVERT: B 984 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8226 (mp) REVERT: B 990 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: B 998 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8376 (p) REVERT: B 1084 ASP cc_start: 0.8045 (t0) cc_final: 0.7692 (t0) REVERT: B 1125 ASN cc_start: 0.8115 (p0) cc_final: 0.7831 (m-40) REVERT: C 99 ASN cc_start: 0.8014 (t0) cc_final: 0.7573 (p0) REVERT: C 118 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7075 (mt) REVERT: C 270 LEU cc_start: 0.8616 (mp) cc_final: 0.8373 (mt) REVERT: C 317 ASN cc_start: 0.7997 (m-40) cc_final: 0.7694 (m-40) REVERT: C 364 ASP cc_start: 0.8149 (t70) cc_final: 0.7698 (t0) REVERT: C 420 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7254 (t0) REVERT: C 423 TYR cc_start: 0.8183 (t80) cc_final: 0.7954 (t80) REVERT: C 428 ASP cc_start: 0.7958 (p0) cc_final: 0.7665 (p0) REVERT: C 539 VAL cc_start: 0.8701 (p) cc_final: 0.8372 (m) REVERT: C 574 ASP cc_start: 0.8515 (t70) cc_final: 0.8169 (t0) REVERT: C 719 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8199 (p) REVERT: C 720 ILE cc_start: 0.8422 (pt) cc_final: 0.8164 (mt) REVERT: C 808 ASP cc_start: 0.8005 (t0) cc_final: 0.7691 (t0) REVERT: C 934 ILE cc_start: 0.8610 (mm) cc_final: 0.8308 (tp) REVERT: C 945 LEU cc_start: 0.8198 (mm) cc_final: 0.7956 (mp) REVERT: C 976 VAL cc_start: 0.8636 (p) cc_final: 0.8397 (m) REVERT: C 990 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7874 (tp30) REVERT: C 1017 GLU cc_start: 0.7994 (tp30) cc_final: 0.7674 (tp30) REVERT: X 81 MET cc_start: 0.5365 (tmm) cc_final: 0.4672 (tmm) REVERT: X 118 MET cc_start: 0.3069 (tpt) cc_final: 0.2705 (tpt) REVERT: Y 4 MET cc_start: 0.5889 (pmm) cc_final: 0.3576 (tpt) REVERT: Z 15 GLU cc_start: 0.4360 (OUTLIER) cc_final: 0.4108 (mm-30) REVERT: U 81 MET cc_start: 0.7104 (tpt) cc_final: 0.6755 (tpt) REVERT: V 147 GLN cc_start: 0.3011 (OUTLIER) cc_final: 0.1947 (tm-30) REVERT: R 118 MET cc_start: 0.1264 (tpt) cc_final: 0.0286 (tpt) REVERT: T 43 MET cc_start: -0.4309 (mmm) cc_final: -0.5267 (tmm) outliers start: 130 outliers final: 110 residues processed: 611 average time/residue: 0.2039 time to fit residues: 212.0313 Evaluate side-chains 640 residues out of total 4091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 515 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 152 VAL Chi-restraints excluded: chain Y residue 19 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 115 VAL Chi-restraints excluded: chain Z residue 15 GLU Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 46 PHE Chi-restraints excluded: chain Z residue 92 MET Chi-restraints excluded: chain Z residue 102 VAL Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 126 THR Chi-restraints excluded: chain V residue 21 ILE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 147 GLN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 191 VAL Chi-restraints excluded: chain S residue 194 CYS Chi-restraints excluded: chain S residue 199 GLN Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 30 optimal weight: 3.9990 chunk 452 optimal weight: 7.9990 chunk 152 optimal weight: 0.1980 chunk 257 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 449 optimal weight: 6.9990 chunk 419 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 305 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 425 optimal weight: 8.9990 overall best weight: 0.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 69 HIS A 762 GLN A 955 ASN B 196 ASN B 755 GLN C 69 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 784 GLN C 935 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 6 GLN U 59 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.212135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152535 restraints weight = 59952.772| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.51 r_work: 0.3576 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37090 Z= 0.136 Angle : 0.582 12.000 50680 Z= 0.297 Chirality : 0.045 0.252 5886 Planarity : 0.004 0.060 6480 Dihedral : 4.703 55.224 5864 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.34 % Allowed : 19.85 % Favored : 76.81 % 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: -0.49 (0.12), residues: 4666 helix: 1.97 (0.20), residues: 679 sheet: 0.05 (0.13), residues: 1432 loop : -1.22 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 466 TYR 0.024 0.001 TYR C 501 PHE 0.050 0.001 PHE B 643 TRP 0.018 0.001 TRP V 35 HIS 0.007 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00322 (36997) covalent geometry : angle 0.56845 (50455) SS BOND : bond 0.00445 ( 54) SS BOND : angle 2.12926 ( 108) hydrogen bonds : bond 0.03797 ( 1384) hydrogen bonds : angle 5.22860 ( 3756) link_BETA1-4 : bond 0.00283 ( 2) link_BETA1-4 : angle 1.05984 ( 6) link_NAG-ASN : bond 0.00320 ( 37) link_NAG-ASN : angle 1.76003 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14280.28 seconds wall clock time: 243 minutes 25.86 seconds (14605.86 seconds total)