Starting phenix.real_space_refine on Sun Jun 29 12:45:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgl_34741/06_2025/8hgl_34741.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgl_34741/06_2025/8hgl_34741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hgl_34741/06_2025/8hgl_34741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgl_34741/06_2025/8hgl_34741.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgl_34741/06_2025/8hgl_34741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgl_34741/06_2025/8hgl_34741.cif" } resolution = 2.9 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= 0.017 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 147 5.16 5 C 21669 2.51 5 N 5631 2.21 5 O 6723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34170 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7784 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "B" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7784 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7784 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1668 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "G" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} 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: "M" 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 23.12, per 1000 atoms: 0.68 Number of scatterers: 34170 At special positions: 0 Unit cell: (138.414, 138.414, 260.406, 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 147 16.00 O 6723 8.00 N 5631 7.00 C 21669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 20 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 20 " - pdb=" SG CYS F 94 " distance=2.04 Simple disulfide: pdb=" SG CYS F 99 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 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 282 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B1134 " " NAG E1301 " - " ASN E 282 " " NAG E1302 " - " ASN E 61 " " NAG E1303 " - " ASN E 122 " " NAG E1304 " - " ASN E 165 " " NAG E1305 " - " ASN E 234 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E1098 " " NAG E1312 " - " ASN E1134 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN E 331 " " NAG S 1 " - " ASN E 343 " " NAG T 1 " - " ASN E 717 " " NAG U 1 " - " ASN E 801 " Time building additional restraints: 10.20 Conformation dependent library (CDL) restraints added in 4.8 seconds 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 77 sheets defined 20.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.718A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.020A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.709A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.609A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.879A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.557A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.506A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.706A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.765A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'H' and resid 26 through 29 removed outlier: 3.820A pdb=" N TYR H 29 " --> pdb=" O THR H 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 26 through 29' Processing helix chain 'H' and resid 85 through 89 Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.994A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.001A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.774A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.563A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.889A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.563A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.552A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.541A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.667A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.787A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.974A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.738A pdb=" N LYS D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.697A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 370 removed outlier: 4.008A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.506A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.555A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.863A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 removed outlier: 3.516A pdb=" N ILE E 870 " --> pdb=" O THR E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 890 removed outlier: 3.559A pdb=" N ALA E 890 " --> pdb=" O THR E 887 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 removed outlier: 4.011A pdb=" N SER E 939 " --> pdb=" O GLN E 935 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 967 removed outlier: 3.891A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL E 952 " --> pdb=" O LEU E 948 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 955 " --> pdb=" O VAL E 951 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 956 " --> pdb=" O VAL E 952 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.511A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.738A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 993 " --> pdb=" O ALA E 989 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP E 994 " --> pdb=" O GLU E 990 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 996 " --> pdb=" O GLN E 992 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E1006 " --> pdb=" O GLN E1002 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR E1007 " --> pdb=" O SER E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1145 Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.968A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 128 Processing helix chain 'G' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.778A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.325A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 51 removed outlier: 4.124A 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: 3.605A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.939A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.286A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.741A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.519A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.925A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.576A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.642A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.227A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.638A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.611A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AC2, first strand: chain 'H' and resid 8 through 10 removed outlier: 6.782A pdb=" N VAL H 32 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP H 48 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 8 through 10 Processing sheet with id=AC4, first strand: chain 'H' and resid 128 through 132 removed outlier: 3.774A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 128 through 132 removed outlier: 3.774A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.133A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.615A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN L 161 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AD2, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.561A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.170A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AD5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.572A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 119 through 122 removed outlier: 3.547A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.935A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.304A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 574 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.689A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.269A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.660A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.049A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.648A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AF1, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.799A pdb=" N VAL C 32 " --> pdb=" O TRP C 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TRP C 48 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP C 34 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AF3, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.773A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 128 through 132 removed outlier: 3.773A pdb=" N GLY C 147 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AF6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.171A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.638A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 161 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AG1, first strand: chain 'E' and resid 28 through 30 removed outlier: 7.912A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 93 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 90 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE E 203 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 47 through 51 removed outlier: 4.180A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AG4, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.607A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 241 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASN E 121 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU E 118 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E 130 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 311 through 319 removed outlier: 6.969A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.767A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AG8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AG9, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 711 through 713 removed outlier: 3.670A pdb=" N THR E1076 " --> pdb=" O SER E1097 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.516A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.668A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AH5, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=AH6, first strand: chain 'F' and resid 8 through 10 removed outlier: 6.793A pdb=" N VAL F 32 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP F 48 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 8 through 10 removed outlier: 3.500A pdb=" N LEU F 110 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.771A pdb=" N GLY F 147 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.771A pdb=" N GLY F 147 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 159 through 162 removed outlier: 3.506A pdb=" N THR F 159 " --> pdb=" O ASN F 207 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AI3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.141A pdb=" N LEU G 11 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.626A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN G 161 " --> pdb=" O THR G 179 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 154 through 155 1363 hydrogen bonds defined for protein. 3633 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: 22.70 Time building geometry restraints manager: 11.98 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: 10766 1.34 - 1.46: 7769 1.46 - 1.58: 16220 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 34935 Sorted by residual: bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.34e+00 bond pdb=" C1 NAG E1304 " pdb=" O5 NAG E1304 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG B1312 " pdb=" O5 NAG B1312 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.58e+00 ... (remaining 34930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 45919 1.64 - 3.28: 1432 3.28 - 4.92: 160 4.92 - 6.56: 41 6.56 - 8.20: 7 Bond angle restraints: 47559 Sorted by residual: angle pdb=" C ASN E 122 " pdb=" CA ASN E 122 " pdb=" CB ASN E 122 " ideal model delta sigma weight residual 111.68 103.48 8.20 1.68e+00 3.54e-01 2.38e+01 angle pdb=" C ASN E 234 " pdb=" CA ASN E 234 " pdb=" CB ASN E 234 " ideal model delta sigma weight residual 110.74 118.02 -7.28 1.61e+00 3.86e-01 2.05e+01 angle pdb=" C LYS F 151 " pdb=" N ASP F 152 " pdb=" CA ASP F 152 " ideal model delta sigma weight residual 122.46 128.47 -6.01 1.41e+00 5.03e-01 1.82e+01 angle pdb=" C LYS C 151 " pdb=" N ASP C 152 " pdb=" CA ASP C 152 " ideal model delta sigma weight residual 122.46 128.47 -6.01 1.41e+00 5.03e-01 1.81e+01 angle pdb=" C LYS H 151 " pdb=" N ASP H 152 " pdb=" CA ASP H 152 " ideal model delta sigma weight residual 122.82 128.51 -5.69 1.42e+00 4.96e-01 1.61e+01 ... (remaining 47554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 20300 22.06 - 44.12: 1092 44.12 - 66.18: 184 66.18 - 88.24: 55 88.24 - 110.31: 26 Dihedral angle restraints: 21657 sinusoidal: 9132 harmonic: 12525 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.87 66.87 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS E 538 " pdb=" SG CYS E 538 " pdb=" SG CYS E 590 " pdb=" CB CYS E 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.33 66.33 1 1.00e+01 1.00e-02 5.75e+01 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 -149.30 63.30 1 1.00e+01 1.00e-02 5.29e+01 ... (remaining 21654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4830 0.077 - 0.154: 722 0.154 - 0.231: 21 0.231 - 0.308: 2 0.308 - 0.384: 2 Chirality restraints: 5577 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C1 NAG E1303 " pdb=" ND2 ASN E 122 " pdb=" C2 NAG E1303 " pdb=" O5 NAG E1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 5574 not shown) Planarity restraints: 6114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 122 " -0.006 2.00e-02 2.50e+03 5.11e-02 3.26e+01 pdb=" CG ASN E 122 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN E 122 " 0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN E 122 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG E1303 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.003 2.00e-02 2.50e+03 4.63e-02 2.68e+01 pdb=" CG ASN E 234 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " 0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.046 2.00e-02 2.50e+03 pdb=" C1 NAG E1305 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " 0.004 2.00e-02 2.50e+03 4.22e-02 2.23e+01 pdb=" CG ASN B 717 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " 0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.044 2.00e-02 2.50e+03 ... (remaining 6111 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2072 2.73 - 3.27: 33123 3.27 - 3.81: 52689 3.81 - 4.36: 61870 4.36 - 4.90: 110122 Nonbonded interactions: 259876 Sorted by model distance: nonbonded pdb=" OD1 ASN L 139 " pdb=" OG1 THR L 173 " model vdw 2.181 3.040 nonbonded pdb=" OD1 ASN D 139 " pdb=" OG1 THR D 173 " model vdw 2.182 3.040 nonbonded pdb=" OD1 ASN G 139 " pdb=" OG1 THR G 173 " model vdw 2.196 3.040 nonbonded pdb=" OG SER D 66 " pdb=" OG1 THR D 73 " model vdw 2.198 3.040 nonbonded pdb=" OG SER L 66 " pdb=" OG1 THR L 73 " model vdw 2.201 3.040 ... (remaining 259871 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.510 Check model and map are aligned: 0.250 Set scattering table: 0.360 Process input model: 96.300 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 35049 Z= 0.273 Angle : 0.739 17.049 47847 Z= 0.372 Chirality : 0.050 0.384 5577 Planarity : 0.004 0.047 6066 Dihedral : 14.180 110.306 13449 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.39 (0.13), residues: 4257 helix: 1.28 (0.20), residues: 699 sheet: 0.26 (0.14), residues: 1311 loop : -1.09 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 886 HIS 0.007 0.001 HIS B1064 PHE 0.064 0.002 PHE E 906 TYR 0.044 0.002 TYR B 160 ARG 0.007 0.000 ARG E 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00917 ( 48) link_NAG-ASN : angle 5.06438 ( 144) link_BETA1-4 : bond 0.01258 ( 12) link_BETA1-4 : angle 4.67766 ( 36) hydrogen bonds : bond 0.16317 ( 1300) hydrogen bonds : angle 6.86346 ( 3633) SS BOND : bond 0.00343 ( 54) SS BOND : angle 1.24969 ( 108) covalent geometry : bond 0.00640 (34935) covalent geometry : angle 0.67179 (47559) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 111 TRP cc_start: 0.2761 (m100) cc_final: 0.1056 (m100) REVERT: D 174 TYR cc_start: 0.5804 (m-80) cc_final: 0.5564 (m-80) REVERT: F 29 TYR cc_start: 0.6080 (m-80) cc_final: 0.5745 (m-10) REVERT: G 174 TYR cc_start: 0.5838 (m-80) cc_final: 0.5597 (m-80) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 1.4684 time to fit residues: 480.7003 Evaluate side-chains 146 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 0.7980 chunk 325 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 111 optimal weight: 50.0000 chunk 219 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 389 optimal weight: 40.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 388 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 90 GLN B 66 HIS B 211 ASN B 239 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1071 GLN D 27 GLN E 196 ASN E 239 GLN E 493 GLN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.133311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073331 restraints weight = 89408.299| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 5.81 r_work: 0.2738 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35049 Z= 0.210 Angle : 0.711 14.301 47847 Z= 0.348 Chirality : 0.048 0.274 5577 Planarity : 0.005 0.052 6066 Dihedral : 8.887 78.697 5889 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.28 % Favored : 95.70 % Rotamer: Outliers : 1.02 % Allowed : 7.06 % Favored : 91.92 % 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: -0.30 (0.13), residues: 4257 helix: 1.34 (0.20), residues: 711 sheet: 0.37 (0.14), residues: 1311 loop : -1.08 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 64 HIS 0.004 0.001 HIS A1064 PHE 0.033 0.002 PHE E 906 TYR 0.031 0.002 TYR D 141 ARG 0.015 0.001 ARG F 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00805 ( 48) link_NAG-ASN : angle 4.48415 ( 144) link_BETA1-4 : bond 0.00923 ( 12) link_BETA1-4 : angle 3.46597 ( 36) hydrogen bonds : bond 0.06221 ( 1300) hydrogen bonds : angle 5.64431 ( 3633) SS BOND : bond 0.00267 ( 54) SS BOND : angle 1.03208 ( 108) covalent geometry : bond 0.00505 (34935) covalent geometry : angle 0.66055 (47559) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.8300 (p90) cc_final: 0.8024 (p90) REVERT: A 453 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.7274 (p90) REVERT: L 32 ASN cc_start: 0.8133 (t0) cc_final: 0.7868 (p0) REVERT: B 453 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7687 (p90) REVERT: B 675 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8089 (pp30) REVERT: B 1010 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: C 111 TRP cc_start: 0.2188 (m100) cc_final: 0.0530 (m100) REVERT: E 160 TYR cc_start: 0.4724 (t80) cc_final: 0.4253 (t80) REVERT: E 374 PHE cc_start: 0.8323 (p90) cc_final: 0.7964 (p90) REVERT: G 174 TYR cc_start: 0.5356 (m-80) cc_final: 0.5154 (m-80) outliers start: 38 outliers final: 14 residues processed: 182 average time/residue: 1.4348 time to fit residues: 320.3835 Evaluate side-chains 149 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 185 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 340 optimal weight: 3.9990 chunk 136 optimal weight: 50.0000 chunk 385 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 105 optimal weight: 30.0000 chunk 187 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 228 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 493 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN L 38 GLN B 66 HIS B 115 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.133029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072750 restraints weight = 89557.494| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 5.49 r_work: 0.2730 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 35049 Z= 0.194 Angle : 0.667 13.761 47847 Z= 0.327 Chirality : 0.047 0.243 5577 Planarity : 0.005 0.050 6066 Dihedral : 7.591 59.010 5889 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.58 % Favored : 95.40 % Rotamer: Outliers : 1.66 % Allowed : 9.45 % Favored : 88.89 % 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: -0.22 (0.13), residues: 4257 helix: 1.45 (0.20), residues: 714 sheet: 0.34 (0.14), residues: 1380 loop : -1.01 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 64 HIS 0.004 0.001 HIS A1064 PHE 0.022 0.002 PHE B 168 TYR 0.028 0.002 TYR G 141 ARG 0.012 0.000 ARG L 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00810 ( 48) link_NAG-ASN : angle 4.30572 ( 144) link_BETA1-4 : bond 0.01073 ( 12) link_BETA1-4 : angle 3.50238 ( 36) hydrogen bonds : bond 0.06054 ( 1300) hydrogen bonds : angle 5.40293 ( 3633) SS BOND : bond 0.00258 ( 54) SS BOND : angle 0.98619 ( 108) covalent geometry : bond 0.00469 (34935) covalent geometry : angle 0.61601 (47559) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 143 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8146 (pmm-80) cc_final: 0.7676 (pmm-80) REVERT: A 374 PHE cc_start: 0.8399 (p90) cc_final: 0.8111 (p90) REVERT: A 464 PHE cc_start: 0.8153 (m-80) cc_final: 0.7308 (m-80) REVERT: L 50 TYR cc_start: 0.7838 (p90) cc_final: 0.7515 (p90) REVERT: B 374 PHE cc_start: 0.8298 (p90) cc_final: 0.7906 (p90) REVERT: B 455 LEU cc_start: 0.6986 (mt) cc_final: 0.6784 (mt) REVERT: C 49 MET cc_start: 0.6333 (tmt) cc_final: 0.6106 (tmt) REVERT: C 111 TRP cc_start: 0.2102 (m100) cc_final: 0.0572 (m100) REVERT: D 50 TYR cc_start: 0.7927 (p90) cc_final: 0.7681 (p90) REVERT: E 374 PHE cc_start: 0.8432 (p90) cc_final: 0.7970 (p90) REVERT: G 174 TYR cc_start: 0.5225 (m-80) cc_final: 0.4995 (m-80) outliers start: 62 outliers final: 21 residues processed: 188 average time/residue: 1.1570 time to fit residues: 274.5385 Evaluate side-chains 148 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 352 optimal weight: 0.9980 chunk 244 optimal weight: 0.0060 chunk 139 optimal weight: 9.9990 chunk 365 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 302 optimal weight: 4.9990 chunk 205 optimal weight: 0.4980 chunk 327 optimal weight: 30.0000 chunk 65 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN L 32 ASN L 90 GLN L 138 ASN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 762 GLN E 115 GLN E 134 GLN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.133693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.070813 restraints weight = 89474.373| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.54 r_work: 0.2811 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35049 Z= 0.134 Angle : 0.622 13.606 47847 Z= 0.301 Chirality : 0.045 0.241 5577 Planarity : 0.004 0.088 6066 Dihedral : 6.972 58.310 5889 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.53 % Allowed : 10.92 % Favored : 87.55 % 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: -0.08 (0.13), residues: 4257 helix: 1.69 (0.20), residues: 714 sheet: 0.38 (0.14), residues: 1344 loop : -0.92 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 64 HIS 0.004 0.001 HIS B1064 PHE 0.026 0.001 PHE E 168 TYR 0.031 0.001 TYR A 453 ARG 0.005 0.000 ARG L 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 48) link_NAG-ASN : angle 4.18385 ( 144) link_BETA1-4 : bond 0.01117 ( 12) link_BETA1-4 : angle 3.39381 ( 36) hydrogen bonds : bond 0.05066 ( 1300) hydrogen bonds : angle 5.14866 ( 3633) SS BOND : bond 0.00297 ( 54) SS BOND : angle 0.85255 ( 108) covalent geometry : bond 0.00307 (34935) covalent geometry : angle 0.57047 (47559) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 130 time to evaluate : 4.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.8427 (p90) cc_final: 0.8058 (p90) REVERT: A 464 PHE cc_start: 0.8017 (m-80) cc_final: 0.7322 (m-80) REVERT: A 869 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8184 (mtt) REVERT: H 49 MET cc_start: 0.5966 (tmm) cc_final: 0.5764 (tpt) REVERT: L 50 TYR cc_start: 0.7902 (p90) cc_final: 0.7681 (p90) REVERT: B 374 PHE cc_start: 0.8296 (p90) cc_final: 0.7902 (p90) REVERT: B 675 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8060 (pp30) REVERT: C 49 MET cc_start: 0.6453 (tmt) cc_final: 0.6243 (tmt) REVERT: C 72 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.5536 (mmp) REVERT: E 66 HIS cc_start: 0.6476 (OUTLIER) cc_final: 0.6248 (t-90) REVERT: E 374 PHE cc_start: 0.8510 (p90) cc_final: 0.8004 (p90) REVERT: E 386 LYS cc_start: 0.9515 (tmmm) cc_final: 0.9184 (ptmm) REVERT: E 702 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8408 (tp30) REVERT: F 49 MET cc_start: 0.6493 (ptp) cc_final: 0.5073 (tmt) outliers start: 57 outliers final: 20 residues processed: 169 average time/residue: 1.6066 time to fit residues: 346.1879 Evaluate side-chains 145 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 702 GLU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 222 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 330 optimal weight: 6.9990 chunk 411 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 322 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 377 optimal weight: 0.5980 chunk 108 optimal weight: 50.0000 chunk 207 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN L 32 ASN L 138 ASN L 167 GLN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN E 196 ASN E 360 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.132840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.070166 restraints weight = 89174.829| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.07 r_work: 0.2767 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35049 Z= 0.183 Angle : 0.649 13.716 47847 Z= 0.316 Chirality : 0.046 0.336 5577 Planarity : 0.004 0.060 6066 Dihedral : 6.868 58.413 5889 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.83 % Allowed : 11.65 % Favored : 86.53 % 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 (0.13), residues: 4257 helix: 1.63 (0.20), residues: 714 sheet: 0.37 (0.14), residues: 1344 loop : -0.93 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.005 0.001 HIS B1064 PHE 0.023 0.002 PHE B 168 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00711 ( 48) link_NAG-ASN : angle 4.20336 ( 144) link_BETA1-4 : bond 0.01036 ( 12) link_BETA1-4 : angle 3.40725 ( 36) hydrogen bonds : bond 0.05768 ( 1300) hydrogen bonds : angle 5.15053 ( 3633) SS BOND : bond 0.00219 ( 54) SS BOND : angle 0.90231 ( 108) covalent geometry : bond 0.00444 (34935) covalent geometry : angle 0.59925 (47559) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 124 time to evaluate : 4.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.8372 (p90) cc_final: 0.8120 (p90) REVERT: A 464 PHE cc_start: 0.8030 (m-80) cc_final: 0.7359 (m-80) REVERT: A 869 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8191 (mtt) REVERT: H 72 MET cc_start: 0.6854 (mmp) cc_final: 0.5753 (mmm) REVERT: L 50 TYR cc_start: 0.7947 (p90) cc_final: 0.7734 (p90) REVERT: B 374 PHE cc_start: 0.8381 (p90) cc_final: 0.7975 (p90) REVERT: C 49 MET cc_start: 0.6519 (tmt) cc_final: 0.6260 (tmt) REVERT: C 72 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.5462 (mmp) REVERT: D 50 TYR cc_start: 0.7984 (p90) cc_final: 0.7685 (p90) REVERT: E 374 PHE cc_start: 0.8499 (p90) cc_final: 0.7990 (p90) REVERT: F 49 MET cc_start: 0.6586 (ptp) cc_final: 0.5260 (tmt) outliers start: 68 outliers final: 36 residues processed: 176 average time/residue: 1.1545 time to fit residues: 259.5689 Evaluate side-chains 156 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 206 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 359 optimal weight: 0.5980 chunk 155 optimal weight: 7.9990 chunk 207 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 138 ASN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 606 ASN E 762 GLN F 172 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.133915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.071877 restraints weight = 89057.968| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.19 r_work: 0.2789 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35049 Z= 0.115 Angle : 0.604 13.808 47847 Z= 0.291 Chirality : 0.045 0.530 5577 Planarity : 0.004 0.048 6066 Dihedral : 6.644 58.223 5889 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.53 % Allowed : 12.37 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4257 helix: 1.86 (0.20), residues: 714 sheet: 0.50 (0.14), residues: 1332 loop : -0.89 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 64 HIS 0.003 0.000 HIS E1088 PHE 0.029 0.001 PHE A 168 TYR 0.020 0.001 TYR G 141 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00759 ( 48) link_NAG-ASN : angle 4.07548 ( 144) link_BETA1-4 : bond 0.01145 ( 12) link_BETA1-4 : angle 3.33011 ( 36) hydrogen bonds : bond 0.04657 ( 1300) hydrogen bonds : angle 4.95635 ( 3633) SS BOND : bond 0.00255 ( 54) SS BOND : angle 0.78117 ( 108) covalent geometry : bond 0.00254 (34935) covalent geometry : angle 0.55457 (47559) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 123 time to evaluate : 3.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.8380 (p90) cc_final: 0.8068 (p90) REVERT: A 464 PHE cc_start: 0.8027 (m-80) cc_final: 0.7339 (m-80) REVERT: H 49 MET cc_start: 0.6289 (tmm) cc_final: 0.6040 (tpt) REVERT: H 72 MET cc_start: 0.6825 (mmp) cc_final: 0.5741 (mmm) REVERT: B 374 PHE cc_start: 0.8324 (p90) cc_final: 0.7925 (p90) REVERT: C 49 MET cc_start: 0.6473 (tmt) cc_final: 0.6226 (tmt) REVERT: C 72 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.5420 (mmp) REVERT: E 66 HIS cc_start: 0.6499 (OUTLIER) cc_final: 0.6265 (t-90) REVERT: E 374 PHE cc_start: 0.8519 (p90) cc_final: 0.8002 (p90) REVERT: E 1010 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: F 49 MET cc_start: 0.6551 (ptp) cc_final: 0.5234 (tmt) outliers start: 57 outliers final: 26 residues processed: 163 average time/residue: 1.1682 time to fit residues: 245.5234 Evaluate side-chains 143 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 3.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 184 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 276 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 360 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 385 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 347 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 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 134 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 138 ASN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN G 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.131643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.069321 restraints weight = 89325.685| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 4.67 r_work: 0.2727 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 35049 Z= 0.265 Angle : 0.708 13.675 47847 Z= 0.346 Chirality : 0.048 0.347 5577 Planarity : 0.005 0.048 6066 Dihedral : 6.829 59.496 5889 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.64 % Allowed : 13.12 % Favored : 85.24 % 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: -0.22 (0.13), residues: 4257 helix: 1.49 (0.20), residues: 711 sheet: 0.31 (0.14), residues: 1308 loop : -0.98 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.010 0.001 HIS B1064 PHE 0.027 0.002 PHE B 168 TYR 0.027 0.002 TYR A1067 ARG 0.005 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 48) link_NAG-ASN : angle 4.28346 ( 144) link_BETA1-4 : bond 0.00928 ( 12) link_BETA1-4 : angle 3.47989 ( 36) hydrogen bonds : bond 0.06770 ( 1300) hydrogen bonds : angle 5.24151 ( 3633) SS BOND : bond 0.00234 ( 54) SS BOND : angle 1.03566 ( 108) covalent geometry : bond 0.00656 (34935) covalent geometry : angle 0.66102 (47559) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 114 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7102 (pmt-80) REVERT: A 374 PHE cc_start: 0.8369 (p90) cc_final: 0.8061 (p90) REVERT: A 464 PHE cc_start: 0.8100 (m-80) cc_final: 0.7498 (m-80) REVERT: H 72 MET cc_start: 0.6783 (mmp) cc_final: 0.5973 (mmt) REVERT: B 374 PHE cc_start: 0.8366 (p90) cc_final: 0.7958 (p90) REVERT: B 740 MET cc_start: 0.8833 (ttt) cc_final: 0.8573 (ttt) REVERT: B 786 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8312 (pmtt) REVERT: C 49 MET cc_start: 0.6232 (tmt) cc_final: 0.5978 (tmt) REVERT: C 72 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.5175 (mmp) REVERT: E 374 PHE cc_start: 0.8522 (p90) cc_final: 0.8023 (p90) outliers start: 61 outliers final: 35 residues processed: 161 average time/residue: 1.1369 time to fit residues: 232.4231 Evaluate side-chains 148 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 184 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 9.9990 chunk 428 optimal weight: 30.0000 chunk 247 optimal weight: 8.9990 chunk 357 optimal weight: 2.9990 chunk 414 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 chunk 328 optimal weight: 5.9990 chunk 139 optimal weight: 30.0000 chunk 213 optimal weight: 0.9980 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 138 ASN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN E 493 GLN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.132558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.069413 restraints weight = 88423.514| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.57 r_work: 0.2782 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35049 Z= 0.164 Angle : 0.644 14.137 47847 Z= 0.311 Chirality : 0.046 0.597 5577 Planarity : 0.004 0.048 6066 Dihedral : 6.696 59.427 5889 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.45 % Allowed : 13.61 % Favored : 84.94 % 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: -0.12 (0.13), residues: 4257 helix: 1.63 (0.20), residues: 714 sheet: 0.41 (0.14), residues: 1332 loop : -0.98 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 64 HIS 0.004 0.001 HIS B1064 PHE 0.028 0.001 PHE A 168 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG D 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 48) link_NAG-ASN : angle 4.17895 ( 144) link_BETA1-4 : bond 0.01080 ( 12) link_BETA1-4 : angle 3.39484 ( 36) hydrogen bonds : bond 0.05645 ( 1300) hydrogen bonds : angle 5.07409 ( 3633) SS BOND : bond 0.00233 ( 54) SS BOND : angle 0.82328 ( 108) covalent geometry : bond 0.00394 (34935) covalent geometry : angle 0.59456 (47559) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.8377 (p90) cc_final: 0.8084 (p90) REVERT: A 464 PHE cc_start: 0.8090 (m-80) cc_final: 0.7471 (m-80) REVERT: A 869 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8168 (mtt) REVERT: H 41 GLN cc_start: 0.5923 (pp30) cc_final: 0.5329 (pp30) REVERT: H 49 MET cc_start: 0.6380 (tmm) cc_final: 0.6174 (tpt) REVERT: H 72 MET cc_start: 0.7123 (mmp) cc_final: 0.6519 (mmt) REVERT: B 374 PHE cc_start: 0.8385 (p90) cc_final: 0.7933 (p90) REVERT: B 386 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9026 (pptt) REVERT: B 786 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8297 (pmtt) REVERT: C 49 MET cc_start: 0.6595 (tmt) cc_final: 0.6319 (tmt) REVERT: C 72 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.5465 (mmp) REVERT: E 374 PHE cc_start: 0.8464 (p90) cc_final: 0.7932 (p90) REVERT: E 493 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7178 (pm20) REVERT: F 49 MET cc_start: 0.6424 (ptp) cc_final: 0.5186 (tmt) outliers start: 54 outliers final: 32 residues processed: 161 average time/residue: 1.2066 time to fit residues: 246.1534 Evaluate side-chains 147 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 156 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 375 optimal weight: 0.1980 chunk 104 optimal weight: 7.9990 chunk 257 optimal weight: 50.0000 chunk 349 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 138 ASN B 66 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.132916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.069981 restraints weight = 89186.983| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.53 r_work: 0.2797 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35049 Z= 0.136 Angle : 0.629 13.687 47847 Z= 0.303 Chirality : 0.045 0.415 5577 Planarity : 0.004 0.046 6066 Dihedral : 6.573 58.844 5889 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.32 % Allowed : 13.85 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.13), residues: 4257 helix: 1.76 (0.20), residues: 714 sheet: 0.46 (0.14), residues: 1332 loop : -0.94 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 64 HIS 0.003 0.001 HIS B1064 PHE 0.030 0.001 PHE A 168 TYR 0.024 0.001 TYR H 105 ARG 0.009 0.000 ARG D 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 48) link_NAG-ASN : angle 4.09232 ( 144) link_BETA1-4 : bond 0.01095 ( 12) link_BETA1-4 : angle 3.36157 ( 36) hydrogen bonds : bond 0.05183 ( 1300) hydrogen bonds : angle 4.98721 ( 3633) SS BOND : bond 0.00218 ( 54) SS BOND : angle 0.78589 ( 108) covalent geometry : bond 0.00320 (34935) covalent geometry : angle 0.58114 (47559) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.8253 (p90) cc_final: 0.8009 (p90) REVERT: A 464 PHE cc_start: 0.8080 (m-80) cc_final: 0.7476 (m-80) REVERT: A 869 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8105 (mtt) REVERT: H 72 MET cc_start: 0.7033 (mmp) cc_final: 0.6387 (mmt) REVERT: B 374 PHE cc_start: 0.8397 (p90) cc_final: 0.7915 (p90) REVERT: B 386 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9027 (pptt) REVERT: C 72 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.5284 (mmp) REVERT: E 117 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8002 (tt) REVERT: E 160 TYR cc_start: 0.4591 (t80) cc_final: 0.4154 (t80) REVERT: E 374 PHE cc_start: 0.8487 (p90) cc_final: 0.7929 (p90) REVERT: E 387 LEU cc_start: 0.8802 (mm) cc_final: 0.8418 (tp) REVERT: E 964 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8586 (mtmm) REVERT: F 72 MET cc_start: 0.6958 (mmp) cc_final: 0.5721 (mmt) outliers start: 49 outliers final: 36 residues processed: 149 average time/residue: 1.1460 time to fit residues: 217.1010 Evaluate side-chains 152 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 754 LEU Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain E residue 1043 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 242 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 374 optimal weight: 2.9990 chunk 130 optimal weight: 0.0980 chunk 206 optimal weight: 0.0370 chunk 386 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 426 optimal weight: 30.0000 chunk 305 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 138 ASN L 167 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 32 ASN ** E 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.133489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.070779 restraints weight = 88458.855| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.51 r_work: 0.2820 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35049 Z= 0.122 Angle : 0.616 13.605 47847 Z= 0.295 Chirality : 0.045 0.318 5577 Planarity : 0.004 0.044 6066 Dihedral : 6.415 58.264 5889 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.15 % Allowed : 14.14 % Favored : 84.70 % 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 (0.13), residues: 4257 helix: 1.89 (0.20), residues: 717 sheet: 0.47 (0.14), residues: 1380 loop : -0.87 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 34 HIS 0.003 0.000 HIS B1064 PHE 0.029 0.001 PHE A 168 TYR 0.030 0.001 TYR E 160 ARG 0.006 0.000 ARG D 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 48) link_NAG-ASN : angle 4.00530 ( 144) link_BETA1-4 : bond 0.01082 ( 12) link_BETA1-4 : angle 3.28609 ( 36) hydrogen bonds : bond 0.04637 ( 1300) hydrogen bonds : angle 4.84339 ( 3633) SS BOND : bond 0.00213 ( 54) SS BOND : angle 0.72616 ( 108) covalent geometry : bond 0.00282 (34935) covalent geometry : angle 0.56904 (47559) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 3.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.8358 (p90) cc_final: 0.8092 (p90) REVERT: A 464 PHE cc_start: 0.8016 (m-80) cc_final: 0.7372 (m-80) REVERT: A 492 LEU cc_start: 0.8597 (mp) cc_final: 0.8203 (tp) REVERT: A 869 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8050 (mtt) REVERT: H 49 MET cc_start: 0.6403 (tmm) cc_final: 0.6173 (tpt) REVERT: H 72 MET cc_start: 0.7078 (mmp) cc_final: 0.6456 (mmt) REVERT: B 374 PHE cc_start: 0.8449 (p90) cc_final: 0.7990 (p90) REVERT: B 386 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9022 (pptt) REVERT: D 30 ASN cc_start: 0.7146 (OUTLIER) cc_final: 0.6850 (p0) REVERT: E 66 HIS cc_start: 0.6553 (OUTLIER) cc_final: 0.6350 (t-90) REVERT: E 374 PHE cc_start: 0.8597 (p90) cc_final: 0.8031 (p90) REVERT: E 387 LEU cc_start: 0.8767 (mm) cc_final: 0.8369 (tp) REVERT: E 964 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8510 (mtmm) REVERT: E 1010 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8431 (mp10) REVERT: F 72 MET cc_start: 0.7068 (mmp) cc_final: 0.5810 (mmt) outliers start: 43 outliers final: 30 residues processed: 153 average time/residue: 1.2124 time to fit residues: 237.0685 Evaluate side-chains 152 residues out of total 3753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 964 LYS Chi-restraints excluded: chain E residue 1010 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 180 optimal weight: 0.9990 chunk 296 optimal weight: 0.3980 chunk 326 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 50.0000 chunk 355 optimal weight: 0.8980 chunk 265 optimal weight: 7.9990 chunk 103 optimal weight: 50.0000 chunk 339 optimal weight: 0.0370 chunk 228 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN L 138 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 501 ASN ** 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 = 0.4295 r_free = 0.4295 target = 0.133914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.070138 restraints weight = 88982.300| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.99 r_work: 0.2863 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 35049 Z= 0.110 Angle : 0.616 15.746 47847 Z= 0.296 Chirality : 0.045 0.295 5577 Planarity : 0.004 0.040 6066 Dihedral : 6.356 58.762 5889 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.02 % Allowed : 14.39 % Favored : 84.59 % 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: 0.15 (0.13), residues: 4257 helix: 2.01 (0.20), residues: 717 sheet: 0.50 (0.14), residues: 1383 loop : -0.82 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 64 HIS 0.003 0.000 HIS E1088 PHE 0.026 0.001 PHE E 133 TYR 0.054 0.001 TYR E 160 ARG 0.006 0.000 ARG D 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 48) link_NAG-ASN : angle 3.94880 ( 144) link_BETA1-4 : bond 0.01210 ( 12) link_BETA1-4 : angle 3.26564 ( 36) hydrogen bonds : bond 0.04295 ( 1300) hydrogen bonds : angle 4.78722 ( 3633) SS BOND : bond 0.00339 ( 54) SS BOND : angle 1.09377 ( 108) covalent geometry : bond 0.00242 (34935) covalent geometry : angle 0.56936 (47559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37184.82 seconds wall clock time: 639 minutes 28.22 seconds (38368.22 seconds total)