Starting phenix.real_space_refine on Fri May 23 08:09:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y7j_33667/05_2025/7y7j_33667.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y7j_33667/05_2025/7y7j_33667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y7j_33667/05_2025/7y7j_33667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y7j_33667/05_2025/7y7j_33667.map" model { file = "/net/cci-nas-00/data/ceres_data/7y7j_33667/05_2025/7y7j_33667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y7j_33667/05_2025/7y7j_33667.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 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 96 5.16 5 C 14973 2.51 5 N 3930 2.21 5 O 4743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23742 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7245 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 48, 'TRANS': 953} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 609 Unresolved non-hydrogen angles: 774 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 15, 'GLU:plan': 7, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 390 Chain: "B" Number of atoms: 7086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7086 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'PTRANS': 48, 'TRANS': 924} Chain breaks: 13 Unresolved non-hydrogen bonds: 549 Unresolved non-hydrogen angles: 699 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 338 Chain: "C" Number of atoms: 6908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 6908 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 13 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 952 Unresolved non-hydrogen dihedrals: 649 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 8, 'TRP:plan': 4, 'ASP:plan': 18, 'PHE:plan': 19, 'GLU:plan': 11, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 499 Chain: "E" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 960 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 759 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: "L" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.17, per 1000 atoms: 0.64 Number of scatterers: 23742 At special positions: 0 Unit cell: (135.3, 135.3, 236.16, 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 96 16.00 O 4743 8.00 N 3930 7.00 C 14973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 122 " " NAG A1306 " - " ASN A 165 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 122 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 122 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 709 " " NAG L 1 " - " ASN B 717 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN B1074 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1074 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 709 " Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 3.0 seconds 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5972 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 46 sheets defined 24.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.599A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.713A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.464A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.421A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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: 3.707A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.771A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 881 Processing helix chain 'A' and resid 884 through 890 removed outlier: 3.556A pdb=" N THR A 887 " --> pdb=" O SER A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.760A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.216A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.058A 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: 3.586A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.536A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.840A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.042A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.024A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.859A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 removed outlier: 4.104A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.515A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.887A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.822A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.537A 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 338 through 343 removed outlier: 3.555A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 5.305A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.745A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.776A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.878A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 888 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.139A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.679A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'D' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.808A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.739A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.228A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.253A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 327 removed outlier: 5.698A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.573A 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 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.147A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.260A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.466A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.333A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.670A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1098 removed outlier: 4.191A pdb=" N HIS A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.191A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.858A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.702A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.135A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 323 through 326 removed outlier: 6.153A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.526A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.506A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 451 through 453 removed outlier: 4.168A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.371A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.101A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.101A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B1113 " --> pdb=" O VAL B1104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.583A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.015A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.615A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.686A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 224 through 227 removed outlier: 3.650A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.601A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.327A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 326 through 328 Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.138A pdb=" N PHE C 515 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.528A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 451 through 453 removed outlier: 4.283A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.583A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.436A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.436A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.510A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.662A pdb=" N TRP E 36 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER E 52 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP E 38 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.736A pdb=" N THR D 109 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 12 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP D 87 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR D 93 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP D 34 " --> pdb=" O TYR D 93 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP D 37 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.736A pdb=" N THR D 109 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 12 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 17 through 23 1009 hydrogen bonds defined for protein. 2721 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: 10.61 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7701 1.34 - 1.47: 6266 1.47 - 1.60: 10108 1.60 - 1.73: 1 1.73 - 1.86: 111 Bond restraints: 24187 Sorted by residual: bond pdb=" C1 NAG A1306 " pdb=" C2 NAG A1306 " ideal model delta sigma weight residual 1.532 1.634 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" CA ASN B 165 " pdb=" C ASN B 165 " ideal model delta sigma weight residual 1.523 1.591 -0.068 1.34e-02 5.57e+03 2.58e+01 bond pdb=" CA ASN B 165 " pdb=" CB ASN B 165 " ideal model delta sigma weight residual 1.530 1.582 -0.052 1.69e-02 3.50e+03 9.39e+00 bond pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.40e+00 bond pdb=" C THR A 478 " pdb=" N PRO A 479 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.39e+00 ... (remaining 24182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 31869 2.38 - 4.77: 1069 4.77 - 7.15: 102 7.15 - 9.54: 24 9.54 - 11.92: 4 Bond angle restraints: 33068 Sorted by residual: angle pdb=" N ALA B 163 " pdb=" CA ALA B 163 " pdb=" C ALA B 163 " ideal model delta sigma weight residual 110.44 102.16 8.28 1.20e+00 6.94e-01 4.76e+01 angle pdb=" C GLY B 648 " pdb=" N CYS B 649 " pdb=" CA CYS B 649 " ideal model delta sigma weight residual 122.93 113.29 9.64 1.45e+00 4.76e-01 4.42e+01 angle pdb=" N PHE A 490 " pdb=" CA PHE A 490 " pdb=" CB PHE A 490 " ideal model delta sigma weight residual 109.59 102.05 7.54 1.21e+00 6.83e-01 3.88e+01 angle pdb=" C TYR A 489 " pdb=" N PHE A 490 " pdb=" CA PHE A 490 " ideal model delta sigma weight residual 122.29 131.37 -9.08 1.48e+00 4.57e-01 3.77e+01 angle pdb=" C PRO A 491 " pdb=" N LEU A 492 " pdb=" CA LEU A 492 " ideal model delta sigma weight residual 122.03 111.61 10.42 2.01e+00 2.48e-01 2.69e+01 ... (remaining 33063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14042 18.00 - 35.99: 777 35.99 - 53.99: 190 53.99 - 71.98: 58 71.98 - 89.98: 17 Dihedral angle restraints: 15084 sinusoidal: 5847 harmonic: 9237 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 -27.79 -58.21 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -36.39 -49.61 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" N ASN B 165 " pdb=" C ASN B 165 " pdb=" CA ASN B 165 " pdb=" CB ASN B 165 " ideal model delta harmonic sigma weight residual 122.80 136.73 -13.93 0 2.50e+00 1.60e-01 3.10e+01 ... (remaining 15081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.567: 4092 0.567 - 1.133: 2 1.133 - 1.700: 2 1.700 - 2.266: 0 2.266 - 2.833: 1 Chirality restraints: 4097 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-02 2.50e+03 6.81e+03 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-02 2.50e+03 2.44e+03 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-02 2.50e+03 1.87e+03 ... (remaining 4094 not shown) Planarity restraints: 4291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 2 " -0.349 2.00e-02 2.50e+03 2.99e-01 1.11e+03 pdb=" C7 NAG Q 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG Q 2 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG Q 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG Q 2 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.329 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG I 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.496 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " 0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " 0.193 2.00e-02 2.50e+03 1.59e-01 3.17e+02 pdb=" C7 NAG T 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " -0.259 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " -0.021 2.00e-02 2.50e+03 ... (remaining 4288 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 243 2.59 - 3.16: 20957 3.16 - 3.74: 33784 3.74 - 4.32: 45854 4.32 - 4.90: 75764 Nonbonded interactions: 176602 Sorted by model distance: nonbonded pdb=" OD1 ASP E 120 " pdb=" CD PRO E 121 " model vdw 2.008 3.440 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.210 3.040 nonbonded pdb=" NE1 TRP A 353 " pdb=" O GLU A 465 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.249 3.040 ... (remaining 176597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 57 or (resid 58 and (name N or nam \ e CA or name C or name O or name CB )) or resid 59 through 66 or resid 81 throug \ h 82 or (resid 83 through 84 and (name N or name CA or name C or name O or name \ CB )) or resid 85 or (resid 86 and (name N or name CA or name C or name O or nam \ e CB )) or resid 87 through 95 or (resid 99 through 100 and (name N or name CA o \ r name C or name O or name CB )) or resid 101 or (resid 102 and (name N or name \ CA or name C or name O or name CB )) or resid 103 or (resid 104 through 106 and \ (name N or name CA or name C or name O or name CB )) or resid 107 through 132 or \ (resid 133 through 136 and (name N or name CA or name C or name O or name CB )) \ or resid 137 through 140 or (resid 157 through 161 and (name N or name CA or na \ me C or name O or name CB )) or resid 162 through 168 or (resid 169 and (name N \ or name CA or name C or name O or name CB )) or resid 170 through 187 or (resid \ 188 and (name N or name CA or name C or name O or name CB )) or resid 189 throug \ h 194 or (resid 195 through 198 and (name N or name CA or name C or name O or na \ me CB )) or resid 199 or (resid 200 and (name N or name CA or name C or name O o \ r name CB )) or resid 201 through 209 or resid 217 through 236 or (resid 237 thr \ ough 241 and (name N or name CA or name C or name O or name CB )) or resid 242 t \ hrough 243 or resid 264 through 268 or (resid 269 and (name N or name CA or name \ C or name O or name CB )) or resid 270 through 274 or (resid 275 and (name N or \ name CA or name C or name O or name CB )) or resid 276 through 315 or (resid 31 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 317 or (resi \ d 318 through 320 and (name N or name CA or name C or name O or name CB )) or re \ sid 321 through 337 or (resid 338 and (name N or name CA or name C or name O or \ name CB )) or resid 339 or (resid 340 and (name N or name CA or name C or name O \ or name CB )) or resid 341 through 344 or (resid 345 through 349 and (name N or \ name CA or name C or name O or name CB )) or resid 350 through 352 or (resid 35 \ 3 through 357 and (name N or name CA or name C or name O or name CB )) or resid \ 358 through 364 or (resid 365 and (name N or name CA or name C or name O or name \ CB )) or resid 366 or (resid 367 through 369 and (name N or name CA or name C o \ r name O or name CB )) or resid 370 through 373 or (resid 374 and (name N or nam \ e CA or name C or name O or name CB )) or resid 375 or (resid 376 through 378 an \ d (name N or name CA or name C or name O or name CB )) or resid 379 through 392 \ or (resid 393 and (name N or name CA or name C or name O or name CB )) or resid \ 394 through 397 or (resid 398 and (name N or name CA or name C or name O or name \ CB )) or resid 399 through 405 or (resid 406 through 411 and (name N or name CA \ or name C or name O or name CB )) or resid 412 through 416 or (resid 417 and (n \ ame N or name CA or name C or name O or name CB )) or resid 418 through 422 or ( \ resid 423 through 424 and (name N or name CA or name C or name O or name CB )) o \ r resid 425 through 440 or (resid 441 through 442 and (name N or name CA or name \ C or name O or name CB )) or resid 443 or (resid 449 through 454 and (name N or \ name CA or name C or name O or name CB )) or resid 460 through 464 or (resid 46 \ 5 through 469 and (name N or name CA or name C or name O or name CB )) or resid \ 470 or (resid 471 and (name N or name CA or name C or name O or name CB )) or re \ sid 487 through 491 or (resid 492 through 495 and (name N or name CA or name C o \ r name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or nam \ e CA or name C or name O or name CB )) or resid 503 through 507 or (resid 508 th \ rough 509 and (name N or name CA or name C or name O or name CB )) or resid 510 \ through 515 or (resid 516 and (name N or name CA or name C or name O or name CB \ )) or resid 517 through 518 or (resid 519 through 520 and (name N or name CA or \ name C or name O or name CB )) or resid 521 through 532 or (resid 533 and (name \ N or name CA or name C or name O or name CB )) or resid 534 or (resid 535 and (n \ ame N or name CA or name C or name O or name CB )) or resid 536 through 541 or ( \ resid 542 through 544 and (name N or name CA or name C or name O or name CB )) o \ r resid 545 or (resid 546 and (name N or name CA or name C or name O or name CB \ )) or resid 547 through 551 or (resid 552 and (name N or name CA or name C or na \ me O or name CB )) or resid 553 or (resid 554 through 555 and (name N or name CA \ or name C or name O or name CB )) or resid 556 through 583 or (resid 584 throug \ h 585 and (name N or name CA or name C or name O or name CB )) or resid 586 thro \ ugh 591 or (resid 592 and (name N or name CA or name C or name O or name CB )) o \ r resid 593 through 612 or (resid 613 through 614 and (name N or name CA or name \ C or name O or name CB )) or resid 615 through 620 or resid 641 through 660 or \ (resid 661 through 663 and (name N or name CA or name C or name O or name CB )) \ or resid 664 through 665 or (resid 666 and (name N or name CA or name C or name \ O or name CB )) or resid 667 through 694 or (resid 695 through 697 and (name N o \ r name CA or name C or name O or name CB )) or resid 698 or (resid 699 and (name \ N or name CA or name C or name O or name CB )) or resid 700 through 703 or (res \ id 704 and (name N or name CA or name C or name O or name CB )) or resid 705 thr \ ough 715 or (resid 716 and (name N or name CA or name C or name O or name CB )) \ or resid 717 through 725 or (resid 726 through 727 and (name N or name CA or nam \ e C or name O or name CB )) or resid 728 or (resid 729 and (name N or name CA or \ name C or name O or name CB )) or resid 730 through 738 or (resid 739 and (name \ N or name CA or name C or name O or name CB )) or resid 740 through 741 or (res \ id 742 and (name N or name CA or name C or name O or name CB )) or resid 743 thr \ ough 751 or (resid 752 through 753 and (name N or name CA or name C or name O or \ name CB )) or resid 754 or (resid 755 and (name N or name CA or name C or name \ O or name CB )) or resid 756 through 774 or (resid 775 and (name N or name CA or \ name C or name O or name CB )) or resid 776 through 785 or (resid 786 and (name \ N or name CA or name C or name O or name CB )) or resid 787 through 789 or (res \ id 790 and (name N or name CA or name C or name O or name CB )) or resid 791 thr \ ough 803 or (resid 804 through 805 and (name N or name CA or name C or name O or \ name CB )) or resid 806 through 853 or (resid 854 and (name N or name CA or nam \ e C or name O or name CB )) or resid 855 through 864 or (resid 865 and (name N o \ r name CA or name C or name O or name CB )) or resid 866 through 868 or (resid 8 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 870 through \ 885 or (resid 886 and (name N or name CA or name C or name O or name CB )) or r \ esid 887 through 904 or (resid 905 through 906 and (name N or name CA or name C \ or name O or name CB )) or resid 907 through 915 or (resid 916 and (name N or na \ me CA or name C or name O or name CB )) or resid 917 through 934 or (resid 935 a \ nd (name N or name CA or name C or name O or name CB )) or resid 936 through 946 \ or (resid 947 and (name N or name CA or name C or name O or name CB )) or resid \ 948 through 972 or (resid 973 through 974 and (name N or name CA or name C or n \ ame O or name CB )) or resid 975 through 978 or (resid 979 and (name N or name C \ A or name C or name O or name CB )) or resid 980 through 982 or (resid 983 and ( \ name N or name CA or name C or name O or name CB )) or resid 984 through 1016 or \ (resid 1017 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 018 through 1028 or (resid 1029 through 1031 and (name N or name CA or name C or \ name O or name CB )) or resid 1032 through 1035 or (resid 1036 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1037 or (resid 1038 through 10 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 1040 throug \ h 1041 or (resid 1042 and (name N or name CA or name C or name O or name CB )) o \ r resid 1043 through 1046 or (resid 1047 through 1050 and (name N or name CA or \ name C or name O or name CB )) or resid 1051 through 1061 or (resid 1062 and (na \ me N or name CA or name C or name O or name CB )) or resid 1063 or (resid 1064 t \ hrough 1065 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 66 through 1071 or (resid 1072 through 1073 and (name N or name CA or name C or \ name O or name CB )) or resid 1074 through 1080 or (resid 1081 and (name N or na \ me CA or name C or name O or name CB )) or resid 1082 through 1083 or (resid 108 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 1085 or (res \ id 1086 through 1089 and (name N or name CA or name C or name O or name CB )) or \ resid 1090 through 1094 or (resid 1095 and (name N or name CA or name C or name \ O or name CB )) or resid 1096 or (resid 1097 and (name N or name CA or name C o \ r name O or name CB )) or resid 1098 through 1099 or (resid 1100 through 1104 an \ d (name N or name CA or name C or name O or name CB )) or resid 1105 through 111 \ 0 or (resid 1111 and (name N or name CA or name C or name O or name CB )) or res \ id 1112 or (resid 1113 through 1116 and (name N or name CA or name C or name O o \ r name CB )) or resid 1117 through 1118 or (resid 1119 through 1120 and (name N \ or name CA or name C or name O or name CB )) or resid 1121 through 1124 or (resi \ d 1125 and (name N or name CA or name C or name O or name CB )) or resid 1126 or \ (resid 1127 through 1128 and (name N or name CA or name C or name O or name CB \ )) or resid 1129 through 1131 or (resid 1132 and (name N or name CA or name C or \ name O or name CB )) or resid 1133 through 1137 or (resid 1138 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1139 through 1146 or resid 130 \ 1 through 1308)) selection = (chain 'B' and (resid 27 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 63 or (resid 64 and (name N or nam \ e CA or name C or name O or name CB )) or resid 65 through 83 or (resid 84 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 or (resid 86 and \ (name N or name CA or name C or name O or name CB )) or resid 87 through 95 or \ resid 99 through 103 or (resid 104 through 106 and (name N or name CA or name C \ or name O or name CB )) or resid 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 112 or (resid 113 and (name N o \ r name CA or name C or name O or name CB )) or resid 114 through 116 or (resid 1 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 118 through \ 129 or (resid 130 and (name N or name CA or name C or name O or name CB )) or r \ esid 131 through 135 or (resid 136 and (name N or name CA or name C or name O or \ name CB )) or resid 137 through 140 or (resid 157 through 161 and (name N or na \ me CA or name C or name O or name CB )) or resid 162 through 175 or (resid 176 t \ hrough 188 and (name N or name CA or name C or name O or name CB )) or resid 189 \ or (resid 190 and (name N or name CA or name C or name O or name CB )) or resid \ 191 through 236 or (resid 237 through 241 and (name N or name CA or name C or n \ ame O or name CB )) or resid 242 through 264 or (resid 265 through 266 and (name \ N or name CA or name C or name O or name CB )) or resid 267 through 268 or (res \ id 269 and (name N or name CA or name C or name O or name CB )) or resid 270 thr \ ough 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) \ or resid 276 through 289 or (resid 290 and (name N or name CA or name C or name \ O or name CB )) or resid 291 through 298 or (resid 299 and (name N or name CA or \ name C or name O or name CB )) or resid 300 through 301 or (resid 302 through 3 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 305 through \ 308 or (resid 309 through 310 and (name N or name CA or name C or name O or nam \ e CB )) or resid 311 through 314 or (resid 315 through 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 or (resid 318 through 320 and ( \ name N or name CA or name C or name O or name CB )) or resid 321 through 324 or \ (resid 325 through 326 and (name N or name CA or name C or name O or name CB )) \ or resid 327 through 328 or resid 335 through 337 or (resid 338 and (name N or n \ ame CA or name C or name O or name CB )) or resid 339 through 341 or (resid 342 \ and (name N or name CA or name C or name O or name CB )) or resid 343 through 34 \ 6 or (resid 347 through 349 and (name N or name CA or name C or name O or name C \ B )) or resid 350 or (resid 351 through 357 and (name N or name CA or name C or \ name O or name CB )) or resid 358 through 363 or (resid 364 through 365 and (nam \ e N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 thro \ ugh 369 and (name N or name CA or name C or name O or name CB )) or resid 370 th \ rough 373 or (resid 374 and (name N or name CA or name C or name O or name CB )) \ or resid 375 through 376 or (resid 377 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 through 386 or (resid 387 and (nam \ e N or name CA or name C or name O or name CB )) or resid 388 through 392 or (re \ sid 393 and (name N or name CA or name C or name O or name CB )) or resid 394 th \ rough 399 or (resid 400 and (name N or name CA or name C or name O or name CB )) \ or resid 401 through 408 or (resid 409 through 411 and (name N or name CA or na \ me C or name O or name CB )) or resid 412 through 420 or (resid 421 through 424 \ and (name N or name CA or name C or name O or name CB )) or resid 425 through 42 \ 8 or (resid 429 and (name N or name CA or name C or name O or name CB )) or resi \ d 430 through 441 or (resid 442 and (name N or name CA or name C or name O or na \ me CB )) or resid 443 through 449 or (resid 450 through 460 and (name N or name \ CA or name C or name O or name CB )) or resid 461 or (resid 462 through 469 and \ (name N or name CA or name C or name O or name CB )) or resid 470 through 471 or \ resid 487 through 493 or (resid 494 through 495 and (name N or name CA or name \ C or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or \ name CA or name C or name O or name CB )) or resid 503 through 508 or (resid 509 \ and (name N or name CA or name C or name O or name CB )) or resid 510 through 5 \ 27 or (resid 528 through 530 and (name N or name CA or name C or name O or name \ CB )) or resid 531 through 532 or (resid 533 and (name N or name CA or name C or \ name O or name CB )) or resid 534 or (resid 535 and (name N or name CA or name \ C or name O or name CB )) or resid 536 through 538 or (resid 539 through 540 and \ (name N or name CA or name C or name O or name CB )) or resid 541 or (resid 542 \ through 544 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 45 or (resid 546 and (name N or name CA or name C or name O or name CB )) or res \ id 547 through 551 or (resid 552 and (name N or name CA or name C or name O or n \ ame CB )) or resid 553 through 563 or (resid 564 and (name N or name CA or name \ C or name O or name CB )) or resid 565 through 575 or (resid 576 through 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 591 o \ r (resid 592 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 93 through 598 or (resid 599 and (name N or name CA or name C or name O or name \ CB )) or resid 600 through 612 or (resid 613 through 614 and (name N or name CA \ or name C or name O or name CB )) or resid 615 through 620 or resid 641 through \ 661 or (resid 662 through 663 and (name N or name CA or name C or name O or name \ CB )) or resid 664 through 715 or (resid 716 and (name N or name CA or name C o \ r name O or name CB )) or resid 717 through 719 or (resid 720 and (name N or nam \ e CA or name C or name O or name CB )) or resid 721 through 728 or (resid 729 an \ d (name N or name CA or name C or name O or name CB )) or resid 730 through 731 \ or (resid 732 through 733 and (name N or name CA or name C or name O or name CB \ )) or resid 734 through 773 or (resid 774 through 775 and (name N or name CA or \ name C or name O or name CB )) or resid 776 or (resid 777 and (name N or name CA \ or name C or name O or name CB )) or resid 778 through 779 or (resid 780 throug \ h 781 and (name N or name CA or name C or name O or name CB )) or resid 782 thro \ ugh 789 or (resid 790 and (name N or name CA or name C or name O or name CB )) o \ r resid 791 through 801 or (resid 802 and (name N or name CA or name C or name O \ or name CB )) or resid 803 through 804 or (resid 805 and (name N or name CA or \ name C or name O or name CB )) or resid 806 through 859 or (resid 860 through 86 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 862 through \ 868 or (resid 869 and (name N or name CA or name C or name O or name CB )) or re \ sid 870 through 885 or (resid 886 and (name N or name CA or name C or name O or \ name CB )) or resid 887 through 901 or (resid 902 through 903 and (name N or nam \ e CA or name C or name O or name CB )) or resid 904 or (resid 905 through 906 an \ d (name N or name CA or name C or name O or name CB )) or resid 907 through 915 \ or (resid 916 and (name N or name CA or name C or name O or name CB )) or resid \ 917 through 921 or (resid 922 and (name N or name CA or name C or name O or name \ CB )) or resid 923 through 925 or (resid 926 through 927 and (name N or name CA \ or name C or name O or name CB )) or resid 928 through 954 or (resid 955 throug \ h 956 and (name N or name CA or name C or name O or name CB )) or resid 957 thro \ ugh 969 or (resid 970 and (name N or name CA or name C or name O or name CB )) o \ r (resid 971 through 974 and (name N or name CA or name C or name O or name CB ) \ ) or resid 975 through 978 or (resid 979 and (name N or name CA or name C or nam \ e O or name CB )) or resid 980 through 982 or (resid 983 and (name N or name CA \ or name C or name O or name CB )) or resid 984 or (resid 985 and (name N or name \ CA or name C or name O or name CB )) or resid 986 through 1010 or (resid 1011 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1012 through 10 \ 13 or (resid 1014 through 1017 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1018 or (resid 1019 through 1020 and (name N or name CA or name \ C or name O or name CB )) or resid 1021 through 1023 or (resid 1024 through 102 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 1027 or (res \ id 1028 through 1031 and (name N or name CA or name C or name O or name CB )) or \ resid 1032 through 1035 or (resid 1036 and (name N or name CA or name C or name \ O or name CB )) or resid 1037 or (resid 1038 through 1039 and (name N or name C \ A or name C or name O or name CB )) or resid 1040 or (resid 1041 through 1042 an \ d (name N or name CA or name C or name O or name CB )) or resid 1043 through 104 \ 4 or (resid 1045 and (name N or name CA or name C or name O or name CB )) or res \ id 1046 or (resid 1047 through 1050 and (name N or name CA or name C or name O o \ r name CB )) or resid 1051 or (resid 1052 and (name N or name CA or name C or na \ me O or name CB )) or resid 1053 through 1061 or (resid 1062 and (name N or name \ CA or name C or name O or name CB )) or resid 1063 or (resid 1064 through 1065 \ and (name N or name CA or name C or name O or name CB )) or resid 1066 through 1 \ 071 or (resid 1072 through 1073 and (name N or name CA or name C or name O or na \ me CB )) or resid 1074 or (resid 1075 and (name N or name CA or name C or name O \ or name CB )) or resid 1076 through 1096 or (resid 1097 and (name N or name CA \ or name C or name O or name CB )) or resid 1098 through 1124 or (resid 1125 and \ (name N or name CA or name C or name O or name CB )) or resid 1126 or (resid 112 \ 7 through 1128 and (name N or name CA or name C or name O or name CB )) or resid \ 1129 through 1131 or (resid 1132 and (name N or name CA or name C or name O or \ name CB )) or resid 1133 through 1146 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 63 or (resid 64 and ( \ name N or name CA or name C or name O or name CB )) or resid 65 through 66 or re \ sid 81 through 82 or (resid 83 through 84 and (name N or name CA or name C or na \ me O or name CB )) or resid 85 through 95 or (resid 99 through 100 and (name N o \ r name CA or name C or name O or name CB )) or resid 101 through 104 or (resid 1 \ 05 through 106 and (name N or name CA or name C or name O or name CB )) or resid \ 107 or (resid 108 and (name N or name CA or name C or name O or name CB )) or r \ esid 109 through 112 or (resid 113 and (name N or name CA or name C or name O or \ name CB )) or resid 114 through 116 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 through 129 or (resid 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 132 or (resid 1 \ 33 through 136 and (name N or name CA or name C or name O or name CB )) or resid \ 137 through 168 or (resid 169 and (name N or name CA or name C or name O or nam \ e CB )) or resid 170 through 187 or (resid 188 and (name N or name CA or name C \ or name O or name CB )) or resid 189 through 199 or (resid 200 and (name N or na \ me CA or name C or name O or name CB )) or resid 201 through 209 or resid 217 th \ rough 243 or (resid 264 through 266 and (name N or name CA or name C or name O o \ r name CB )) or resid 267 through 298 or (resid 299 and (name N or name CA or na \ me C or name O or name CB )) or resid 300 through 301 or (resid 302 through 304 \ and (name N or name CA or name C or name O or name CB )) or resid 305 through 30 \ 8 or (resid 309 through 310 and (name N or name CA or name C or name O or name C \ B )) or resid 311 through 314 or (resid 315 through 316 and (name N or name CA o \ r name C or name O or name CB )) or resid 317 through 319 or (resid 320 and (nam \ e N or name CA or name C or name O or name CB )) or resid 321 through 323 or (re \ sid 324 through 326 and (name N or name CA or name C or name O or name CB )) or \ resid 327 through 328 or resid 335 through 344 or (resid 345 through 349 and (na \ me N or name CA or name C or name O or name CB )) or resid 350 through 356 or (r \ esid 357 and (name N or name CA or name C or name O or name CB )) or resid 358 t \ hrough 375 or (resid 376 through 378 and (name N or name CA or name C or name O \ or name CB )) or resid 379 or (resid 380 and (name N or name CA or name C or nam \ e O or name CB )) or resid 381 through 399 or (resid 400 and (name N or name CA \ or name C or name O or name CB )) or resid 401 through 408 or (resid 409 through \ 411 and (name N or name CA or name C or name O or name CB )) or resid 412 throu \ gh 420 or (resid 421 through 424 and (name N or name CA or name C or name O or n \ ame CB )) or resid 425 through 428 or (resid 429 and (name N or name CA or name \ C or name O or name CB )) or resid 430 through 449 or (resid 450 through 460 and \ (name N or name CA or name C or name O or name CB )) or resid 461 or (resid 462 \ through 469 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 70 through 493 or (resid 494 through 495 and (name N or name CA or name C or nam \ e O or name CB )) or resid 496 through 504 or (resid 505 and (name N or name CA \ or name C or name O or name CB )) or resid 506 through 507 or (resid 508 through \ 509 and (name N or name CA or name C or name O or name CB )) or resid 510 throu \ gh 536 or (resid 537 and (name N or name CA or name C or name O or name CB )) or \ resid 538 or (resid 539 through 540 and (name N or name CA or name C or name O \ or name CB )) or resid 541 through 542 or (resid 543 through 544 and (name N or \ name CA or name C or name O or name CB )) or resid 545 through 554 or (resid 555 \ and (name N or name CA or name C or name O or name CB )) or resid 556 through 5 \ 63 or (resid 564 and (name N or name CA or name C or name O or name CB )) or res \ id 565 through 575 or (resid 576 through 578 and (name N or name CA or name C or \ name O or name CB )) or resid 579 or (resid 580 through 581 and (name N or name \ CA or name C or name O or name CB )) or resid 582 or (resid 583 through 585 and \ (name N or name CA or name C or name O or name CB )) or resid 586 through 598 o \ r (resid 599 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 00 through 660 or (resid 661 through 663 and (name N or name CA or name C or nam \ e O or name CB )) or resid 664 through 665 or (resid 666 and (name N or name CA \ or name C or name O or name CB )) or resid 667 through 695 or (resid 696 through \ 697 and (name N or name CA or name C or name O or name CB )) or resid 698 or (r \ esid 699 and (name N or name CA or name C or name O or name CB )) or resid 700 t \ hrough 702 or (resid 703 through 704 and (name N or name CA or name C or name O \ or name CB )) or resid 705 through 719 or (resid 720 and (name N or name CA or n \ ame C or name O or name CB )) or resid 721 through 725 or (resid 726 through 727 \ and (name N or name CA or name C or name O or name CB )) or resid 728 through 7 \ 31 or (resid 732 through 733 and (name N or name CA or name C or name O or name \ CB )) or resid 734 through 738 or (resid 739 and (name N or name CA or name C or \ name O or name CB )) or resid 740 through 741 or (resid 742 and (name N or name \ CA or name C or name O or name CB )) or resid 743 through 751 or (resid 752 thr \ ough 753 and (name N or name CA or name C or name O or name CB )) or resid 754 o \ r (resid 755 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 56 through 773 or (resid 774 through 775 and (name N or name CA or name C or nam \ e O or name CB )) or resid 776 or (resid 777 and (name N or name CA or name C or \ name O or name CB )) or resid 778 through 785 or (resid 786 and (name N or name \ CA or name C or name O or name CB )) or resid 787 through 801 or (resid 802 and \ (name N or name CA or name C or name O or name CB )) or resid 803 or (resid 804 \ through 805 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 06 through 853 or (resid 854 and (name N or name CA or name C or name O or name \ CB )) or resid 855 through 859 or (resid 860 through 861 and (name N or name CA \ or name C or name O or name CB )) or resid 862 through 921 or (resid 922 and (na \ me N or name CA or name C or name O or name CB )) or resid 923 through 925 or (r \ esid 926 through 927 and (name N or name CA or name C or name O or name CB )) or \ resid 928 through 934 or (resid 935 and (name N or name CA or name C or name O \ or name CB )) or resid 936 through 946 or (resid 947 and (name N or name CA or n \ ame C or name O or name CB )) or resid 948 through 954 or (resid 955 through 956 \ and (name N or name CA or name C or name O or name CB )) or resid 957 through 9 \ 69 or (resid 970 and (name N or name CA or name C or name O or name CB )) or res \ id 971 through 984 or (resid 985 and (name N or name CA or name C or name O or n \ ame CB )) or resid 986 through 1010 or (resid 1011 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1012 through 1013 or (resid 1014 through 10 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 1018 or (re \ sid 1019 through 1020 and (name N or name CA or name C or name O or name CB )) o \ r resid 1021 through 1029 or (resid 1030 through 1031 and (name N or name CA or \ name C or name O or name CB )) or resid 1032 through 1033 or (resid 1034 and (na \ me N or name CA or name C or name O or name CB )) or resid 1035 through 1044 or \ (resid 1045 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 46 through 1074 or (resid 1075 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1076 through 1080 or (resid 1081 and (name N or name CA or name \ C or name O or name CB )) or resid 1082 through 1083 or (resid 1084 and (name N \ or name CA or name C or name O or name CB )) or resid 1085 or (resid 1086 throu \ gh 1089 and (name N or name CA or name C or name O or name CB )) or resid 1090 t \ hrough 1099 or (resid 1100 through 1104 and (name N or name CA or name C or name \ O or name CB )) or resid 1105 through 1110 or (resid 1111 and (name N or name C \ A or name C or name O or name CB )) or resid 1112 or (resid 1113 through 1116 an \ d (name N or name CA or name C or name O or name CB )) or resid 1117 through 111 \ 8 or (resid 1119 through 1120 and (name N or name CA or name C or name O or name \ CB )) or resid 1121 through 1136 or (resid 1137 through 1138 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1139 through 1146 or resid 1301 \ through 1308)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.500 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: 0.010 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 57.500 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.140 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.008 0.195 24280 Z= 0.345 Angle : 1.222 42.420 33310 Z= 0.609 Chirality : 0.084 2.833 4097 Planarity : 0.010 0.299 4250 Dihedral : 12.735 89.975 9001 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.56 % Favored : 93.66 % Rotamer: Outliers : 1.09 % Allowed : 3.58 % Favored : 95.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3109 helix: -0.06 (0.20), residues: 643 sheet: -0.83 (0.19), residues: 673 loop : -1.89 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 886 HIS 0.011 0.002 HIS E 100 PHE 0.024 0.002 PHE A 490 TYR 0.042 0.003 TYR E 35 ARG 0.028 0.001 ARG D 63 Details of bonding type rmsd link_NAG-ASN : bond 0.03631 ( 41) link_NAG-ASN : angle 6.73741 ( 123) link_BETA1-4 : bond 0.05411 ( 15) link_BETA1-4 : angle 15.93352 ( 45) hydrogen bonds : bond 0.13854 ( 989) hydrogen bonds : angle 7.84524 ( 2721) SS BOND : bond 0.00702 ( 37) SS BOND : angle 2.23079 ( 74) covalent geometry : bond 0.00725 (24187) covalent geometry : angle 0.98874 (33068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 PHE cc_start: 0.8698 (m-10) cc_final: 0.8169 (m-80) REVERT: B 394 ASN cc_start: 0.7739 (m-40) cc_final: 0.7379 (m-40) REVERT: C 229 LEU cc_start: 0.9183 (mp) cc_final: 0.8939 (tp) REVERT: C 505 TYR cc_start: 0.8824 (m-80) cc_final: 0.8472 (t80) REVERT: D 41 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6569 (tp) REVERT: D 75 LEU cc_start: 0.5568 (tp) cc_final: 0.5120 (tp) outliers start: 25 outliers final: 5 residues processed: 203 average time/residue: 0.3505 time to fit residues: 114.2212 Evaluate side-chains 82 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain D residue 16 GLN Chi-restraints excluded: chain D residue 41 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 288 optimal weight: 0.1980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 493 GLN A 501 ASN A 542 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 755 GLN A 901 GLN A 907 ASN A 965 GLN A1101 HIS B 66 HIS B 207 HIS B 564 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 954 GLN B 955 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 66 HIS C 271 GLN C 536 ASN C 606 ASN C 644 GLN C 751 ASN C 755 GLN C 955 ASN C 965 GLN C1101 HIS C1113 GLN E 100 HIS D 33 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.082284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057387 restraints weight = 117857.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.059097 restraints weight = 66871.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059242 restraints weight = 40232.349| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24280 Z= 0.141 Angle : 0.741 23.446 33310 Z= 0.363 Chirality : 0.050 1.034 4097 Planarity : 0.004 0.048 4250 Dihedral : 8.510 59.972 4519 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.96 % Favored : 95.88 % Rotamer: Outliers : 1.53 % Allowed : 7.90 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 3109 helix: 1.63 (0.21), residues: 651 sheet: -0.38 (0.19), residues: 675 loop : -1.55 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 122 HIS 0.003 0.001 HIS B 655 PHE 0.026 0.001 PHE A 490 TYR 0.022 0.001 TYR B 904 ARG 0.006 0.000 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 41) link_NAG-ASN : angle 3.27551 ( 123) link_BETA1-4 : bond 0.00442 ( 15) link_BETA1-4 : angle 2.68851 ( 45) hydrogen bonds : bond 0.05806 ( 989) hydrogen bonds : angle 5.96066 ( 2721) SS BOND : bond 0.00362 ( 37) SS BOND : angle 1.20361 ( 74) covalent geometry : bond 0.00285 (24187) covalent geometry : angle 0.70680 (33068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 2.867 Fit side-chains revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8421 (m-10) cc_final: 0.8148 (m-10) REVERT: A 1002 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7192 (tm-30) REVERT: A 1031 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: B 365 TYR cc_start: 0.8693 (m-80) cc_final: 0.8063 (m-80) REVERT: C 229 LEU cc_start: 0.9285 (mp) cc_final: 0.9047 (tp) REVERT: C 505 TYR cc_start: 0.8986 (m-80) cc_final: 0.8528 (t80) REVERT: C 740 MET cc_start: 0.8713 (mmm) cc_final: 0.8440 (tpt) REVERT: E 113 ARG cc_start: 0.5672 (ttt180) cc_final: 0.5163 (ttt90) REVERT: E 120 ASP cc_start: 0.6519 (OUTLIER) cc_final: 0.5653 (t0) REVERT: D 75 LEU cc_start: 0.5373 (tp) cc_final: 0.4773 (tp) outliers start: 35 outliers final: 13 residues processed: 127 average time/residue: 0.3338 time to fit residues: 71.9396 Evaluate side-chains 90 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 109 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 98 optimal weight: 0.0370 chunk 244 optimal weight: 9.9990 chunk 229 optimal weight: 0.8980 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 913 GLN A1002 GLN B 644 GLN B 762 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 388 ASN C 935 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.081890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057021 restraints weight = 118042.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058565 restraints weight = 68535.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058932 restraints weight = 39583.980| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24280 Z= 0.125 Angle : 0.649 19.456 33310 Z= 0.320 Chirality : 0.047 0.774 4097 Planarity : 0.004 0.060 4250 Dihedral : 7.514 59.023 4513 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 2.01 % Allowed : 9.42 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3109 helix: 1.96 (0.21), residues: 661 sheet: -0.11 (0.19), residues: 691 loop : -1.40 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 122 HIS 0.003 0.001 HIS B 655 PHE 0.028 0.001 PHE B 759 TYR 0.034 0.001 TYR B 904 ARG 0.007 0.000 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 41) link_NAG-ASN : angle 2.80951 ( 123) link_BETA1-4 : bond 0.00327 ( 15) link_BETA1-4 : angle 2.29179 ( 45) hydrogen bonds : bond 0.05024 ( 989) hydrogen bonds : angle 5.39608 ( 2721) SS BOND : bond 0.00333 ( 37) SS BOND : angle 1.37635 ( 74) covalent geometry : bond 0.00267 (24187) covalent geometry : angle 0.61932 (33068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 2.638 Fit side-chains revert: symmetry clash REVERT: A 964 LYS cc_start: 0.9234 (tppt) cc_final: 0.8860 (tppt) REVERT: A 1031 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: B 365 TYR cc_start: 0.8698 (m-80) cc_final: 0.8038 (m-80) REVERT: B 400 PHE cc_start: 0.8715 (p90) cc_final: 0.8191 (p90) REVERT: B 993 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9163 (pt) REVERT: C 229 LEU cc_start: 0.9299 (mp) cc_final: 0.9061 (tp) REVERT: C 505 TYR cc_start: 0.8929 (m-80) cc_final: 0.8494 (t80) REVERT: C 740 MET cc_start: 0.8770 (mmm) cc_final: 0.8352 (tpt) REVERT: C 957 GLN cc_start: 0.8919 (tp40) cc_final: 0.8508 (tm-30) REVERT: E 113 ARG cc_start: 0.5455 (ttt180) cc_final: 0.4898 (ttt90) REVERT: E 120 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.5648 (t0) outliers start: 46 outliers final: 20 residues processed: 115 average time/residue: 0.2931 time to fit residues: 59.4384 Evaluate side-chains 99 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 53 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 304 optimal weight: 30.0000 chunk 182 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 244 optimal weight: 30.0000 chunk 21 optimal weight: 0.3980 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.080720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055826 restraints weight = 118998.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.057262 restraints weight = 69992.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.057292 restraints weight = 42406.368| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24280 Z= 0.159 Angle : 0.642 17.836 33310 Z= 0.316 Chirality : 0.047 0.678 4097 Planarity : 0.004 0.046 4250 Dihedral : 7.203 59.352 4513 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.08 % Rotamer: Outliers : 2.05 % Allowed : 10.51 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3109 helix: 2.03 (0.21), residues: 652 sheet: -0.13 (0.19), residues: 721 loop : -1.29 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 886 HIS 0.005 0.001 HIS A1064 PHE 0.012 0.001 PHE B 238 TYR 0.042 0.001 TYR B 904 ARG 0.003 0.000 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 41) link_NAG-ASN : angle 2.68358 ( 123) link_BETA1-4 : bond 0.00348 ( 15) link_BETA1-4 : angle 1.93541 ( 45) hydrogen bonds : bond 0.05004 ( 989) hydrogen bonds : angle 5.24843 ( 2721) SS BOND : bond 0.00387 ( 37) SS BOND : angle 1.28596 ( 74) covalent geometry : bond 0.00359 (24187) covalent geometry : angle 0.61568 (33068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 80 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8436 (m-10) cc_final: 0.8161 (m-10) REVERT: A 979 ASP cc_start: 0.9094 (m-30) cc_final: 0.8714 (t70) REVERT: A 1031 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: A 1141 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9006 (pt) REVERT: B 400 PHE cc_start: 0.8755 (p90) cc_final: 0.8180 (p90) REVERT: B 993 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9181 (pt) REVERT: C 229 LEU cc_start: 0.9300 (mp) cc_final: 0.9060 (tp) REVERT: C 505 TYR cc_start: 0.8970 (m-80) cc_final: 0.8495 (t80) REVERT: C 740 MET cc_start: 0.8785 (mmm) cc_final: 0.8400 (tpp) outliers start: 47 outliers final: 25 residues processed: 119 average time/residue: 0.2834 time to fit residues: 58.6453 Evaluate side-chains 101 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain D residue 58 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 101 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 297 optimal weight: 30.0000 chunk 195 optimal weight: 0.0010 chunk 158 optimal weight: 1.9990 chunk 230 optimal weight: 30.0000 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.080510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055590 restraints weight = 117573.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.057233 restraints weight = 69077.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.057344 restraints weight = 42217.911| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24280 Z= 0.141 Angle : 0.612 17.381 33310 Z= 0.299 Chirality : 0.046 0.636 4097 Planarity : 0.004 0.046 4250 Dihedral : 6.919 58.796 4511 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.30 % Rotamer: Outliers : 1.88 % Allowed : 12.09 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3109 helix: 2.13 (0.21), residues: 652 sheet: 0.09 (0.19), residues: 698 loop : -1.24 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 49 HIS 0.004 0.001 HIS A1064 PHE 0.011 0.001 PHE A 888 TYR 0.034 0.001 TYR B 904 ARG 0.002 0.000 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 41) link_NAG-ASN : angle 2.50851 ( 123) link_BETA1-4 : bond 0.00298 ( 15) link_BETA1-4 : angle 1.70611 ( 45) hydrogen bonds : bond 0.04736 ( 989) hydrogen bonds : angle 5.08644 ( 2721) SS BOND : bond 0.00352 ( 37) SS BOND : angle 1.18120 ( 74) covalent geometry : bond 0.00315 (24187) covalent geometry : angle 0.58885 (33068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8555 (m-10) cc_final: 0.8343 (m-10) REVERT: A 979 ASP cc_start: 0.9046 (m-30) cc_final: 0.8722 (t70) REVERT: B 400 PHE cc_start: 0.8745 (p90) cc_final: 0.8161 (p90) REVERT: B 993 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9158 (pt) REVERT: C 229 LEU cc_start: 0.9324 (mp) cc_final: 0.9072 (tp) REVERT: C 505 TYR cc_start: 0.8916 (m-80) cc_final: 0.8477 (t80) REVERT: C 740 MET cc_start: 0.8759 (mmm) cc_final: 0.8377 (tpp) outliers start: 43 outliers final: 28 residues processed: 112 average time/residue: 0.3000 time to fit residues: 58.4762 Evaluate side-chains 98 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 316 optimal weight: 40.0000 chunk 69 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 214 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A 913 GLN B 762 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.078344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053527 restraints weight = 117980.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.055080 restraints weight = 70537.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054881 restraints weight = 42333.878| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 24280 Z= 0.278 Angle : 0.734 16.996 33310 Z= 0.363 Chirality : 0.048 0.658 4097 Planarity : 0.004 0.043 4250 Dihedral : 7.294 58.412 4511 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 2.18 % Allowed : 12.35 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3109 helix: 1.64 (0.20), residues: 646 sheet: -0.19 (0.18), residues: 757 loop : -1.37 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 353 HIS 0.006 0.001 HIS A1064 PHE 0.016 0.002 PHE B1052 TYR 0.048 0.002 TYR B 904 ARG 0.006 0.001 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 41) link_NAG-ASN : angle 2.79722 ( 123) link_BETA1-4 : bond 0.00334 ( 15) link_BETA1-4 : angle 1.77039 ( 45) hydrogen bonds : bond 0.05872 ( 989) hydrogen bonds : angle 5.54281 ( 2721) SS BOND : bond 0.00506 ( 37) SS BOND : angle 1.34128 ( 74) covalent geometry : bond 0.00636 (24187) covalent geometry : angle 0.71045 (33068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 67 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.9113 (m-30) cc_final: 0.8790 (t70) REVERT: A 1002 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 400 PHE cc_start: 0.8823 (p90) cc_final: 0.8159 (p90) REVERT: C 505 TYR cc_start: 0.8944 (m-80) cc_final: 0.8451 (t80) REVERT: C 740 MET cc_start: 0.8749 (mmm) cc_final: 0.8519 (tpp) REVERT: C 904 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6595 (t80) outliers start: 50 outliers final: 34 residues processed: 111 average time/residue: 0.2802 time to fit residues: 55.6563 Evaluate side-chains 97 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 47 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 236 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 233 optimal weight: 30.0000 chunk 214 optimal weight: 20.0000 chunk 196 optimal weight: 4.9990 chunk 223 optimal weight: 30.0000 chunk 192 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.078996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.054014 restraints weight = 118179.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055600 restraints weight = 69487.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055598 restraints weight = 43543.471| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24280 Z= 0.168 Angle : 0.638 17.117 33310 Z= 0.311 Chirality : 0.046 0.624 4097 Planarity : 0.004 0.044 4250 Dihedral : 7.037 57.190 4511 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.21 % Favored : 95.72 % Rotamer: Outliers : 1.92 % Allowed : 13.22 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3109 helix: 1.93 (0.21), residues: 647 sheet: -0.04 (0.18), residues: 734 loop : -1.32 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 122 HIS 0.004 0.001 HIS B1064 PHE 0.012 0.001 PHE A 888 TYR 0.033 0.001 TYR B 904 ARG 0.003 0.000 ARG E 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 41) link_NAG-ASN : angle 2.59300 ( 123) link_BETA1-4 : bond 0.00266 ( 15) link_BETA1-4 : angle 1.54617 ( 45) hydrogen bonds : bond 0.05194 ( 989) hydrogen bonds : angle 5.27436 ( 2721) SS BOND : bond 0.00374 ( 37) SS BOND : angle 1.14884 ( 74) covalent geometry : bond 0.00379 (24187) covalent geometry : angle 0.61587 (33068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 67 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.9066 (m-30) cc_final: 0.8756 (t70) REVERT: B 400 PHE cc_start: 0.8807 (p90) cc_final: 0.8055 (p90) REVERT: C 505 TYR cc_start: 0.8877 (m-80) cc_final: 0.8451 (t80) REVERT: C 740 MET cc_start: 0.8665 (mmm) cc_final: 0.8435 (tpp) outliers start: 44 outliers final: 35 residues processed: 106 average time/residue: 0.2928 time to fit residues: 55.4117 Evaluate side-chains 98 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 36 optimal weight: 50.0000 chunk 288 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 235 optimal weight: 30.0000 chunk 246 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 137 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.078582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053623 restraints weight = 118538.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055214 restraints weight = 68657.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.055397 restraints weight = 39527.659| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24280 Z= 0.202 Angle : 0.657 16.816 33310 Z= 0.321 Chirality : 0.047 0.614 4097 Planarity : 0.004 0.048 4250 Dihedral : 7.021 57.181 4511 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 2.01 % Allowed : 13.48 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3109 helix: 1.89 (0.21), residues: 647 sheet: -0.01 (0.19), residues: 722 loop : -1.34 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 886 HIS 0.004 0.001 HIS B1064 PHE 0.047 0.001 PHE B 238 TYR 0.032 0.001 TYR B 904 ARG 0.003 0.000 ARG E 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 41) link_NAG-ASN : angle 2.56240 ( 123) link_BETA1-4 : bond 0.00262 ( 15) link_BETA1-4 : angle 1.49981 ( 45) hydrogen bonds : bond 0.05245 ( 989) hydrogen bonds : angle 5.30310 ( 2721) SS BOND : bond 0.00374 ( 37) SS BOND : angle 1.16651 ( 74) covalent geometry : bond 0.00456 (24187) covalent geometry : angle 0.63556 (33068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.9075 (m-30) cc_final: 0.8751 (t70) REVERT: B 400 PHE cc_start: 0.8855 (p90) cc_final: 0.8428 (p90) outliers start: 46 outliers final: 40 residues processed: 107 average time/residue: 0.2857 time to fit residues: 54.9006 Evaluate side-chains 105 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 65 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 101 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 245 optimal weight: 0.7980 chunk 271 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.080076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055265 restraints weight = 116662.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056937 restraints weight = 67627.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.057083 restraints weight = 40159.462| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24280 Z= 0.105 Angle : 0.590 16.527 33310 Z= 0.286 Chirality : 0.046 0.559 4097 Planarity : 0.004 0.049 4250 Dihedral : 6.566 56.974 4511 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 1.48 % Allowed : 13.87 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3109 helix: 2.38 (0.21), residues: 646 sheet: 0.21 (0.19), residues: 715 loop : -1.20 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.002 0.000 HIS A1064 PHE 0.042 0.001 PHE B 238 TYR 0.022 0.001 TYR B 904 ARG 0.005 0.000 ARG E 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 41) link_NAG-ASN : angle 2.28938 ( 123) link_BETA1-4 : bond 0.00372 ( 15) link_BETA1-4 : angle 1.39193 ( 45) hydrogen bonds : bond 0.04257 ( 989) hydrogen bonds : angle 4.88477 ( 2721) SS BOND : bond 0.00238 ( 37) SS BOND : angle 0.96479 ( 74) covalent geometry : bond 0.00227 (24187) covalent geometry : angle 0.57165 (33068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.9042 (m-30) cc_final: 0.8716 (t70) REVERT: B 400 PHE cc_start: 0.8781 (p90) cc_final: 0.8313 (p90) REVERT: C 957 GLN cc_start: 0.8833 (tp40) cc_final: 0.8622 (tm-30) outliers start: 34 outliers final: 29 residues processed: 111 average time/residue: 0.2916 time to fit residues: 57.2054 Evaluate side-chains 101 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 175 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 177 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 285 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 292 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 261 optimal weight: 0.0000 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.080222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.055412 restraints weight = 117747.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057081 restraints weight = 68219.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057235 restraints weight = 40409.853| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24280 Z= 0.100 Angle : 0.581 15.999 33310 Z= 0.281 Chirality : 0.045 0.542 4097 Planarity : 0.004 0.051 4250 Dihedral : 6.380 56.484 4511 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 1.35 % Allowed : 14.27 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3109 helix: 2.46 (0.21), residues: 643 sheet: 0.33 (0.19), residues: 713 loop : -1.10 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 886 HIS 0.003 0.000 HIS B1048 PHE 0.040 0.001 PHE B 238 TYR 0.025 0.001 TYR B 904 ARG 0.005 0.000 ARG E 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 41) link_NAG-ASN : angle 2.23038 ( 123) link_BETA1-4 : bond 0.00316 ( 15) link_BETA1-4 : angle 1.36796 ( 45) hydrogen bonds : bond 0.04063 ( 989) hydrogen bonds : angle 4.77430 ( 2721) SS BOND : bond 0.00250 ( 37) SS BOND : angle 0.96320 ( 74) covalent geometry : bond 0.00213 (24187) covalent geometry : angle 0.56275 (33068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6218 Ramachandran restraints generated. 3109 Oldfield, 0 Emsley, 3109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.9066 (m-30) cc_final: 0.8728 (t70) REVERT: B 400 PHE cc_start: 0.8768 (p90) cc_final: 0.8289 (p90) REVERT: C 957 GLN cc_start: 0.8819 (tp40) cc_final: 0.8615 (tm-30) outliers start: 31 outliers final: 27 residues processed: 102 average time/residue: 0.2927 time to fit residues: 52.7255 Evaluate side-chains 101 residues out of total 2782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 251 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 303 optimal weight: 20.0000 chunk 205 optimal weight: 0.0030 chunk 181 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.080006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.055090 restraints weight = 116678.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056718 restraints weight = 68128.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056888 restraints weight = 40724.179| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24280 Z= 0.114 Angle : 0.587 15.721 33310 Z= 0.284 Chirality : 0.045 0.543 4097 Planarity : 0.004 0.049 4250 Dihedral : 6.305 56.404 4510 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.53 % Allowed : 14.14 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3109 helix: 2.45 (0.21), residues: 646 sheet: 0.41 (0.19), residues: 718 loop : -1.09 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.003 0.001 HIS A1064 PHE 0.039 0.001 PHE B 238 TYR 0.025 0.001 TYR B 904 ARG 0.005 0.000 ARG E 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 41) link_NAG-ASN : angle 2.19654 ( 123) link_BETA1-4 : bond 0.00280 ( 15) link_BETA1-4 : angle 1.33964 ( 45) hydrogen bonds : bond 0.04125 ( 989) hydrogen bonds : angle 4.76079 ( 2721) SS BOND : bond 0.00251 ( 37) SS BOND : angle 0.94676 ( 74) covalent geometry : bond 0.00257 (24187) covalent geometry : angle 0.56971 (33068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6818.44 seconds wall clock time: 121 minutes 3.80 seconds (7263.80 seconds total)