Starting phenix.real_space_refine on Fri Mar 6 07:33:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0g_24105/03_2026/7n0g_24105_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0g_24105/03_2026/7n0g_24105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n0g_24105/03_2026/7n0g_24105_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0g_24105/03_2026/7n0g_24105_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n0g_24105/03_2026/7n0g_24105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0g_24105/03_2026/7n0g_24105.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 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 126 5.16 5 C 18432 2.51 5 N 4788 2.21 5 O 5716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29062 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8395 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 57, 'TRANS': 1018} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 8405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8405 Classifications: {'peptide': 1078} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 57, 'TRANS': 1020} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8384 Classifications: {'peptide': 1075} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 57, 'TRANS': 1017} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.30, per 1000 atoms: 0.22 Number of scatterers: 29062 At special positions: 0 Unit cell: (163.06, 158.852, 210.4, 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 126 16.00 O 5716 8.00 N 4788 7.00 C 18432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 165 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B1098 " " NAG B1314 " - " ASN B1134 " " NAG B1315 " - " ASN C 282 " " NAG C1301 " - " ASN A 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 149 " " NAG C1306 " - " ASN C 165 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN A 122 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN B 61 " " NAG S 1 " - " ASN B 17 " " NAG U 1 " - " ASN C 17 " " NAG V 1 " - " ASN C 122 " " NAG W 1 " - " ASN C 234 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 61 sheets defined 21.7% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.133A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.585A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.522A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.559A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.539A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.053A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.726A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.710A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.122A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.576A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.748A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' 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 755 removed outlier: 3.646A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.670A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.742A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.861A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.576A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.278A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.924A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.440A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.590A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.538A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.817A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.695A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.529A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.527A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.509A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.829A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.724A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.842A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.917A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'Y' and resid 87 through 91 removed outlier: 3.501A pdb=" N THR Y 91 " --> pdb=" O PRO Y 88 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.327A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.327A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.086A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.975A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.382A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.664A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.783A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.764A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.651A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.172A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.889A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.054A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.415A 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 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.847A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.012A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.012A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.956A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.514A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.814A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.417A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.838A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.358A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.786A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.991A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.628A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.703A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.703A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.505A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.505A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.013A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.488A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.807A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.785A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.735A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.834A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.944A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.510A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.133A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.066A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.335A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'X' and resid 10 through 13 removed outlier: 4.705A pdb=" N LYS X 99 " --> pdb=" O ARG X 33 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG X 33 " --> pdb=" O LYS X 99 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG X 38 " --> pdb=" O TRP X 47 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TRP X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 10 through 13 Processing sheet with id=AG2, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.083A pdb=" N GLY Y 10 " --> pdb=" O THR Y 118 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER Y 120 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL Y 12 " --> pdb=" O SER Y 120 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS Y 99 " --> pdb=" O ARG Y 33 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG Y 33 " --> pdb=" O LYS Y 99 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.083A pdb=" N GLY Y 10 " --> pdb=" O THR Y 118 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER Y 120 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL Y 12 " --> pdb=" O SER Y 120 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 3 through 8 Processing sheet with id=AG6, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.214A pdb=" N GLY Z 10 " --> pdb=" O THR Z 118 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER Z 120 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL Z 12 " --> pdb=" O SER Z 120 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS Z 99 " --> pdb=" O ARG Z 33 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG Z 33 " --> pdb=" O LYS Z 99 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG Z 38 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TRP Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.214A pdb=" N GLY Z 10 " --> pdb=" O THR Z 118 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER Z 120 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL Z 12 " --> pdb=" O SER Z 120 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3258 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: 7.05 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9221 1.34 - 1.46: 6815 1.46 - 1.58: 13526 1.58 - 1.70: 1 1.70 - 1.82: 162 Bond restraints: 29725 Sorted by residual: bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.534 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.492 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 29720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 39632 1.94 - 3.89: 763 3.89 - 5.83: 53 5.83 - 7.78: 11 7.78 - 9.72: 3 Bond angle restraints: 40462 Sorted by residual: angle pdb=" C ASN B 657 " pdb=" CA ASN B 657 " pdb=" CB ASN B 657 " ideal model delta sigma weight residual 109.07 118.79 -9.72 1.68e+00 3.54e-01 3.35e+01 angle pdb=" C ASN B 616 " pdb=" CA ASN B 616 " pdb=" CB ASN B 616 " ideal model delta sigma weight residual 109.33 117.39 -8.06 1.97e+00 2.58e-01 1.67e+01 angle pdb=" C VAL B 615 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 122.81 116.89 5.92 1.57e+00 4.06e-01 1.42e+01 angle pdb=" N ASN B 657 " pdb=" CA ASN B 657 " pdb=" CB ASN B 657 " ideal model delta sigma weight residual 110.67 106.03 4.64 1.39e+00 5.18e-01 1.11e+01 angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 121.54 127.85 -6.31 1.91e+00 2.74e-01 1.09e+01 ... (remaining 40457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.27: 17508 25.27 - 50.55: 765 50.55 - 75.82: 194 75.82 - 101.10: 86 101.10 - 126.37: 64 Dihedral angle restraints: 18617 sinusoidal: 8179 harmonic: 10438 Sorted by residual: dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 165.19 -72.19 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -156.47 70.47 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CA VAL B 656 " pdb=" C VAL B 656 " pdb=" N ASN B 657 " pdb=" CA ASN B 657 " ideal model delta harmonic sigma weight residual 180.00 -140.80 -39.20 0 5.00e+00 4.00e-02 6.15e+01 ... (remaining 18614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.191: 4725 0.191 - 0.381: 14 0.381 - 0.572: 3 0.572 - 0.763: 1 0.763 - 0.953: 2 Chirality restraints: 4745 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 ... (remaining 4742 not shown) Planarity restraints: 5219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.010 2.00e-02 2.50e+03 6.64e-02 5.51e+01 pdb=" CG ASN B 657 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.080 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG B1310 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.023 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" CG ASN B 657 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.033 2.00e-02 2.50e+03 3.28e-02 1.35e+01 pdb=" CG ASN C1074 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.036 2.00e-02 2.50e+03 ... (remaining 5216 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 865 2.71 - 3.25: 28310 3.25 - 3.80: 46094 3.80 - 4.35: 58364 4.35 - 4.90: 99168 Nonbonded interactions: 232801 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.157 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.205 3.040 nonbonded pdb=" NH1 ARG A 357 " pdb=" O CYS B 166 " model vdw 2.216 3.120 nonbonded pdb=" NE2 GLN Z 116 " pdb=" OG1 THR Z 118 " model vdw 2.217 3.120 nonbonded pdb=" OG SER B 366 " pdb=" OD1 ASN B 388 " model vdw 2.235 3.040 ... (remaining 232796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 331 or (resid 332 through 333 and (name N or na \ me CA or name C or name O or name CB )) or resid 334 through 620 or resid 641 th \ rough 1308)) selection = (chain 'B' and (resid 14 through 528 or (resid 529 and (name N or name CA or nam \ e C or name O or name CB )) or resid 530 through 620 or resid 641 through 1308)) \ selection = (chain 'C' and resid 14 through 1308) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 27.120 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.004 0.128 29842 Z= 0.191 Angle : 0.695 19.910 40765 Z= 0.327 Chirality : 0.053 0.953 4745 Planarity : 0.004 0.060 5165 Dihedral : 17.867 126.372 11801 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.03 % Allowed : 0.32 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3562 helix: 2.28 (0.21), residues: 644 sheet: 0.10 (0.16), residues: 1004 loop : -0.47 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.027 0.001 TYR A 904 PHE 0.017 0.001 PHE B 377 TRP 0.011 0.001 TRP A 886 HIS 0.003 0.000 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00384 (29725) covalent geometry : angle 0.60039 (40462) SS BOND : bond 0.00252 ( 42) SS BOND : angle 1.57388 ( 84) hydrogen bonds : bond 0.10212 ( 1162) hydrogen bonds : angle 6.46571 ( 3258) Misc. bond : bond 0.00308 ( 2) link_BETA1-4 : bond 0.00642 ( 19) link_BETA1-4 : angle 2.27291 ( 57) link_NAG-ASN : bond 0.01077 ( 54) link_NAG-ASN : angle 5.31833 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.710 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: B 456 PHE cc_start: 0.9018 (m-80) cc_final: 0.8434 (m-80) REVERT: X 37 TYR cc_start: -0.1331 (m-80) cc_final: -0.1731 (m-10) REVERT: X 60 TYR cc_start: 0.4370 (m-80) cc_final: 0.4016 (m-80) REVERT: X 105 TYR cc_start: -0.0054 (m-10) cc_final: -0.0737 (m-80) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1720 time to fit residues: 38.5656 Evaluate side-chains 106 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 148 ASN A1002 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1005 GLN C 360 ASN C 658 ASN C 762 GLN C 901 GLN C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.153430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.098422 restraints weight = 78067.961| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.48 r_work: 0.3166 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29842 Z= 0.189 Angle : 0.691 18.867 40765 Z= 0.319 Chirality : 0.050 0.541 4745 Planarity : 0.004 0.055 5165 Dihedral : 15.031 108.995 5413 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3562 helix: 2.32 (0.21), residues: 637 sheet: 0.23 (0.16), residues: 1000 loop : -0.54 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 357 TYR 0.030 0.002 TYR A 904 PHE 0.014 0.001 PHE B 342 TRP 0.020 0.001 TRP Y 111 HIS 0.005 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00437 (29725) covalent geometry : angle 0.62853 (40462) SS BOND : bond 0.00287 ( 42) SS BOND : angle 1.44020 ( 84) hydrogen bonds : bond 0.04010 ( 1162) hydrogen bonds : angle 5.50486 ( 3258) Misc. bond : bond 0.00111 ( 2) link_BETA1-4 : bond 0.00676 ( 19) link_BETA1-4 : angle 2.08202 ( 57) link_NAG-ASN : bond 0.00769 ( 54) link_NAG-ASN : angle 4.35144 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.9171 (m-80) cc_final: 0.8631 (m-80) REVERT: B 869 MET cc_start: 0.9298 (mtt) cc_final: 0.9096 (mtt) REVERT: X 34 MET cc_start: 0.1196 (pmm) cc_final: 0.0915 (pmm) REVERT: X 37 TYR cc_start: -0.1572 (m-80) cc_final: -0.1885 (m-10) REVERT: X 60 TYR cc_start: 0.4412 (m-80) cc_final: 0.4028 (m-80) REVERT: Y 32 ASP cc_start: 0.5861 (t70) cc_final: 0.4886 (t0) REVERT: Y 37 TYR cc_start: 0.0734 (m-80) cc_final: 0.0126 (m-10) REVERT: Y 83 MET cc_start: 0.1018 (mmp) cc_final: -0.0206 (mtp) outliers start: 6 outliers final: 2 residues processed: 110 average time/residue: 0.1504 time to fit residues: 28.9841 Evaluate side-chains 101 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain Z residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 0.7980 chunk 297 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 349 optimal weight: 7.9990 chunk 311 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1005 GLN B1135 ASN C 360 ASN C 440 ASN ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.135768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.084084 restraints weight = 75968.710| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.83 r_work: 0.3004 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29842 Z= 0.163 Angle : 0.649 19.208 40765 Z= 0.298 Chirality : 0.049 0.494 4745 Planarity : 0.004 0.052 5165 Dihedral : 12.763 110.607 5413 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.52 % Allowed : 7.18 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3562 helix: 2.26 (0.21), residues: 650 sheet: 0.32 (0.16), residues: 995 loop : -0.51 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.032 0.001 TYR A 904 PHE 0.014 0.001 PHE A 898 TRP 0.014 0.001 TRP Y 111 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00377 (29725) covalent geometry : angle 0.59077 (40462) SS BOND : bond 0.00202 ( 42) SS BOND : angle 1.29287 ( 84) hydrogen bonds : bond 0.03813 ( 1162) hydrogen bonds : angle 5.35392 ( 3258) Misc. bond : bond 0.00080 ( 2) link_BETA1-4 : bond 0.00557 ( 19) link_BETA1-4 : angle 2.20212 ( 57) link_NAG-ASN : bond 0.00743 ( 54) link_NAG-ASN : angle 4.01724 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8263 (tm130) cc_final: 0.8046 (tm-30) REVERT: B 456 PHE cc_start: 0.9119 (m-80) cc_final: 0.8611 (m-80) REVERT: B 869 MET cc_start: 0.9316 (mtt) cc_final: 0.9109 (mtt) REVERT: C 177 MET cc_start: -0.5325 (OUTLIER) cc_final: -0.5660 (ttt) REVERT: X 37 TYR cc_start: -0.1166 (m-80) cc_final: -0.1464 (m-10) REVERT: X 52 TYR cc_start: 0.1928 (m-80) cc_final: 0.1529 (m-10) REVERT: X 60 TYR cc_start: 0.4374 (m-80) cc_final: 0.3903 (m-80) REVERT: Y 83 MET cc_start: 0.1258 (mmp) cc_final: 0.0124 (mtp) outliers start: 16 outliers final: 5 residues processed: 119 average time/residue: 0.1681 time to fit residues: 34.6396 Evaluate side-chains 107 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain Z residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 220 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 360 ASN C 440 ASN C 655 HIS ** Y 113 GLN ** 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 = 0.4277 r_free = 0.4277 target = 0.135783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.082476 restraints weight = 78032.768| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 4.06 r_work: 0.2919 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 29842 Z= 0.374 Angle : 0.755 19.440 40765 Z= 0.355 Chirality : 0.052 0.503 4745 Planarity : 0.004 0.068 5165 Dihedral : 11.816 109.592 5413 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.97 % Allowed : 9.37 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3562 helix: 1.94 (0.21), residues: 653 sheet: 0.17 (0.16), residues: 997 loop : -0.64 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1107 TYR 0.046 0.002 TYR A 904 PHE 0.018 0.002 PHE B 898 TRP 0.010 0.002 TRP A 886 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00883 (29725) covalent geometry : angle 0.70470 (40462) SS BOND : bond 0.00325 ( 42) SS BOND : angle 1.77842 ( 84) hydrogen bonds : bond 0.04644 ( 1162) hydrogen bonds : angle 5.57616 ( 3258) Misc. bond : bond 0.00044 ( 2) link_BETA1-4 : bond 0.00475 ( 19) link_BETA1-4 : angle 2.22841 ( 57) link_NAG-ASN : bond 0.00767 ( 54) link_NAG-ASN : angle 4.01677 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8450 (tm130) cc_final: 0.8238 (tm-30) REVERT: A 1010 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8369 (mp10) REVERT: B 245 HIS cc_start: 0.7898 (m-70) cc_final: 0.7618 (m-70) REVERT: B 456 PHE cc_start: 0.9104 (m-80) cc_final: 0.8558 (m-80) REVERT: C 177 MET cc_start: -0.5180 (OUTLIER) cc_final: -0.5581 (ttt) REVERT: X 37 TYR cc_start: -0.1469 (m-80) cc_final: -0.1785 (m-10) REVERT: X 52 TYR cc_start: 0.1769 (m-80) cc_final: 0.1523 (m-10) REVERT: X 60 TYR cc_start: 0.4570 (m-80) cc_final: 0.4082 (m-80) REVERT: Y 37 TYR cc_start: 0.0477 (m-80) cc_final: 0.0267 (m-80) REVERT: Y 51 ILE cc_start: 0.4681 (OUTLIER) cc_final: 0.4467 (tp) REVERT: Y 83 MET cc_start: 0.1431 (mmp) cc_final: 0.0371 (mtp) outliers start: 30 outliers final: 14 residues processed: 126 average time/residue: 0.1738 time to fit residues: 37.5452 Evaluate side-chains 113 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 83 optimal weight: 0.5980 chunk 278 optimal weight: 0.0870 chunk 45 optimal weight: 30.0000 chunk 243 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN X 103 HIS ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.152654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.098970 restraints weight = 77712.715| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.97 r_work: 0.2957 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29842 Z= 0.119 Angle : 0.624 19.410 40765 Z= 0.287 Chirality : 0.047 0.478 4745 Planarity : 0.003 0.052 5165 Dihedral : 10.917 109.904 5413 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.03 % Allowed : 10.24 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3562 helix: 2.23 (0.21), residues: 647 sheet: 0.27 (0.16), residues: 995 loop : -0.51 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1107 TYR 0.027 0.001 TYR A 904 PHE 0.013 0.001 PHE C 898 TRP 0.010 0.001 TRP Y 111 HIS 0.003 0.000 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00262 (29725) covalent geometry : angle 0.56923 (40462) SS BOND : bond 0.00247 ( 42) SS BOND : angle 1.24229 ( 84) hydrogen bonds : bond 0.03625 ( 1162) hydrogen bonds : angle 5.26357 ( 3258) Misc. bond : bond 0.00021 ( 2) link_BETA1-4 : bond 0.00565 ( 19) link_BETA1-4 : angle 2.20681 ( 57) link_NAG-ASN : bond 0.00688 ( 54) link_NAG-ASN : angle 3.80316 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8574 (t0) REVERT: A 1002 GLN cc_start: 0.8276 (tm130) cc_final: 0.8040 (tm-30) REVERT: B 245 HIS cc_start: 0.7894 (m-70) cc_final: 0.7571 (m-70) REVERT: B 456 PHE cc_start: 0.9096 (m-80) cc_final: 0.8580 (m-80) REVERT: C 177 MET cc_start: -0.5465 (OUTLIER) cc_final: -0.5783 (ttt) REVERT: C 387 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8187 (mm) REVERT: C 957 GLN cc_start: 0.8612 (tt0) cc_final: 0.8345 (tt0) REVERT: X 37 TYR cc_start: -0.1534 (m-80) cc_final: -0.1776 (m-10) REVERT: X 60 TYR cc_start: 0.4352 (m-80) cc_final: 0.3842 (m-80) REVERT: Y 37 TYR cc_start: 0.0733 (m-80) cc_final: 0.0418 (m-80) REVERT: Y 64 VAL cc_start: 0.0655 (OUTLIER) cc_final: 0.0362 (p) REVERT: Y 83 MET cc_start: 0.1622 (mmp) cc_final: 0.0612 (mtp) outliers start: 32 outliers final: 10 residues processed: 132 average time/residue: 0.1647 time to fit residues: 38.0575 Evaluate side-chains 105 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 325 optimal weight: 50.0000 chunk 178 optimal weight: 3.9990 chunk 257 optimal weight: 30.0000 chunk 191 optimal weight: 2.9990 chunk 296 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 334 optimal weight: 0.0980 chunk 84 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Y 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.152161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097205 restraints weight = 77103.753| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.52 r_work: 0.2986 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29842 Z= 0.143 Angle : 0.623 19.623 40765 Z= 0.285 Chirality : 0.047 0.468 4745 Planarity : 0.003 0.051 5165 Dihedral : 10.356 109.888 5413 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.03 % Allowed : 10.47 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3562 helix: 2.35 (0.21), residues: 650 sheet: 0.33 (0.16), residues: 983 loop : -0.48 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 33 TYR 0.026 0.001 TYR X 52 PHE 0.016 0.001 PHE B 490 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00327 (29725) covalent geometry : angle 0.56878 (40462) SS BOND : bond 0.00246 ( 42) SS BOND : angle 1.04905 ( 84) hydrogen bonds : bond 0.03655 ( 1162) hydrogen bonds : angle 5.18243 ( 3258) Misc. bond : bond 0.00010 ( 2) link_BETA1-4 : bond 0.00499 ( 19) link_BETA1-4 : angle 2.17912 ( 57) link_NAG-ASN : bond 0.00652 ( 54) link_NAG-ASN : angle 3.81603 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8578 (t0) REVERT: A 988 GLU cc_start: 0.8596 (pm20) cc_final: 0.8186 (pm20) REVERT: A 1002 GLN cc_start: 0.8282 (tm130) cc_final: 0.8052 (tm-30) REVERT: B 456 PHE cc_start: 0.9076 (m-80) cc_final: 0.8602 (m-80) REVERT: C 152 TRP cc_start: 0.6528 (m100) cc_final: 0.6210 (m100) REVERT: C 177 MET cc_start: -0.5249 (OUTLIER) cc_final: -0.5593 (ttt) REVERT: C 387 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7791 (mm) REVERT: C 957 GLN cc_start: 0.8584 (tt0) cc_final: 0.8288 (tt0) REVERT: X 60 TYR cc_start: 0.4302 (m-80) cc_final: 0.3913 (m-80) REVERT: Y 64 VAL cc_start: 0.0666 (OUTLIER) cc_final: 0.0375 (p) REVERT: Y 83 MET cc_start: 0.1569 (mmp) cc_final: 0.0577 (mtp) REVERT: Y 113 GLN cc_start: 0.4749 (OUTLIER) cc_final: 0.4450 (pm20) outliers start: 32 outliers final: 15 residues processed: 123 average time/residue: 0.1625 time to fit residues: 35.2691 Evaluate side-chains 110 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 113 GLN Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 233 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 192 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 245 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.150835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097931 restraints weight = 77476.597| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.16 r_work: 0.2975 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 29842 Z= 0.238 Angle : 0.660 19.823 40765 Z= 0.307 Chirality : 0.049 0.477 4745 Planarity : 0.004 0.054 5165 Dihedral : 9.964 109.008 5413 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.29 % Allowed : 10.82 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3562 helix: 2.25 (0.21), residues: 649 sheet: 0.27 (0.16), residues: 955 loop : -0.55 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.021 0.001 TYR C 265 PHE 0.016 0.001 PHE A1121 TRP 0.034 0.001 TRP Y 111 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00559 (29725) covalent geometry : angle 0.61007 (40462) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.18633 ( 84) hydrogen bonds : bond 0.04085 ( 1162) hydrogen bonds : angle 5.29492 ( 3258) Misc. bond : bond 0.00035 ( 2) link_BETA1-4 : bond 0.00472 ( 19) link_BETA1-4 : angle 2.15822 ( 57) link_NAG-ASN : bond 0.00654 ( 54) link_NAG-ASN : angle 3.79644 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8629 (t0) REVERT: A 1002 GLN cc_start: 0.8386 (tm130) cc_final: 0.8165 (tm-30) REVERT: B 456 PHE cc_start: 0.9107 (m-80) cc_final: 0.8631 (m-80) REVERT: C 177 MET cc_start: -0.5312 (OUTLIER) cc_final: -0.5587 (ttt) REVERT: C 387 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8180 (mm) REVERT: C 957 GLN cc_start: 0.8660 (tt0) cc_final: 0.8366 (tt0) REVERT: X 60 TYR cc_start: 0.4175 (m-80) cc_final: 0.3763 (m-80) REVERT: Y 64 VAL cc_start: 0.1002 (OUTLIER) cc_final: 0.0684 (p) REVERT: Y 83 MET cc_start: 0.1541 (mmp) cc_final: 0.0537 (mtp) outliers start: 40 outliers final: 23 residues processed: 130 average time/residue: 0.1646 time to fit residues: 37.7995 Evaluate side-chains 123 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Y residue 51 ILE Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 88 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 194 optimal weight: 0.0970 chunk 135 optimal weight: 0.6980 chunk 79 optimal weight: 0.0770 chunk 49 optimal weight: 30.0000 chunk 222 optimal weight: 9.9990 chunk 265 optimal weight: 20.0000 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.138831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.086371 restraints weight = 76855.898| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 4.22 r_work: 0.3010 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29842 Z= 0.106 Angle : 0.602 19.857 40765 Z= 0.277 Chirality : 0.047 0.457 4745 Planarity : 0.003 0.050 5165 Dihedral : 9.372 109.033 5413 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.74 % Allowed : 11.47 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3562 helix: 2.44 (0.21), residues: 644 sheet: 0.35 (0.16), residues: 965 loop : -0.48 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.021 0.001 TYR X 52 PHE 0.011 0.001 PHE C 898 TRP 0.036 0.001 TRP X 111 HIS 0.002 0.000 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00232 (29725) covalent geometry : angle 0.54916 (40462) SS BOND : bond 0.00270 ( 42) SS BOND : angle 0.96635 ( 84) hydrogen bonds : bond 0.03471 ( 1162) hydrogen bonds : angle 5.12490 ( 3258) Misc. bond : bond 0.00020 ( 2) link_BETA1-4 : bond 0.00557 ( 19) link_BETA1-4 : angle 2.14272 ( 57) link_NAG-ASN : bond 0.00663 ( 54) link_NAG-ASN : angle 3.72450 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8427 (t0) REVERT: A 988 GLU cc_start: 0.8619 (pm20) cc_final: 0.8206 (pm20) REVERT: B 456 PHE cc_start: 0.9096 (m-80) cc_final: 0.8580 (m-80) REVERT: C 177 MET cc_start: -0.5649 (OUTLIER) cc_final: -0.5876 (ttt) REVERT: C 387 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7655 (mm) REVERT: C 957 GLN cc_start: 0.8631 (tt0) cc_final: 0.8409 (tt0) REVERT: X 60 TYR cc_start: 0.4067 (m-80) cc_final: 0.3695 (m-80) REVERT: Y 64 VAL cc_start: 0.1084 (OUTLIER) cc_final: 0.0772 (p) REVERT: Y 83 MET cc_start: 0.1692 (mmp) cc_final: 0.0737 (mtp) outliers start: 23 outliers final: 14 residues processed: 120 average time/residue: 0.1671 time to fit residues: 35.4939 Evaluate side-chains 107 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 112 optimal weight: 5.9990 chunk 335 optimal weight: 30.0000 chunk 123 optimal weight: 0.5980 chunk 285 optimal weight: 2.9990 chunk 297 optimal weight: 0.0060 chunk 290 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.136635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.084167 restraints weight = 75259.200| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 4.06 r_work: 0.2968 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29842 Z= 0.177 Angle : 0.623 20.453 40765 Z= 0.288 Chirality : 0.047 0.460 4745 Planarity : 0.003 0.051 5165 Dihedral : 9.090 107.758 5413 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.97 % Allowed : 11.59 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3562 helix: 2.46 (0.21), residues: 644 sheet: 0.40 (0.16), residues: 943 loop : -0.49 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.019 0.001 TYR C 265 PHE 0.015 0.001 PHE B 898 TRP 0.030 0.001 TRP X 111 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00412 (29725) covalent geometry : angle 0.57215 (40462) SS BOND : bond 0.00269 ( 42) SS BOND : angle 1.06759 ( 84) hydrogen bonds : bond 0.03772 ( 1162) hydrogen bonds : angle 5.15974 ( 3258) Misc. bond : bond 0.00030 ( 2) link_BETA1-4 : bond 0.00482 ( 19) link_BETA1-4 : angle 2.08264 ( 57) link_NAG-ASN : bond 0.00620 ( 54) link_NAG-ASN : angle 3.70292 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8383 (t0) REVERT: B 456 PHE cc_start: 0.9112 (m-80) cc_final: 0.8612 (m-80) REVERT: C 177 MET cc_start: -0.5616 (OUTLIER) cc_final: -0.5833 (ttt) REVERT: C 957 GLN cc_start: 0.8626 (tt0) cc_final: 0.8327 (tt0) REVERT: X 60 TYR cc_start: 0.4287 (m-80) cc_final: 0.3864 (m-80) REVERT: Y 64 VAL cc_start: 0.0626 (OUTLIER) cc_final: 0.0343 (p) REVERT: Y 83 MET cc_start: 0.1685 (mmp) cc_final: 0.0733 (mtp) outliers start: 30 outliers final: 19 residues processed: 113 average time/residue: 0.1608 time to fit residues: 32.2727 Evaluate side-chains 111 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 193 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 223 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.151693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097899 restraints weight = 77439.458| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.90 r_work: 0.2930 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29842 Z= 0.182 Angle : 0.629 20.277 40765 Z= 0.292 Chirality : 0.048 0.463 4745 Planarity : 0.003 0.051 5165 Dihedral : 8.765 106.716 5413 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.97 % Allowed : 11.59 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3562 helix: 2.34 (0.21), residues: 651 sheet: 0.34 (0.16), residues: 947 loop : -0.48 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.018 0.001 TYR C 265 PHE 0.015 0.001 PHE A 898 TRP 0.029 0.001 TRP C 152 HIS 0.002 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00424 (29725) covalent geometry : angle 0.57834 (40462) SS BOND : bond 0.00419 ( 42) SS BOND : angle 1.42091 ( 84) hydrogen bonds : bond 0.03786 ( 1162) hydrogen bonds : angle 5.19322 ( 3258) Misc. bond : bond 0.00048 ( 2) link_BETA1-4 : bond 0.00492 ( 19) link_BETA1-4 : angle 2.03572 ( 57) link_NAG-ASN : bond 0.00626 ( 54) link_NAG-ASN : angle 3.69446 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8513 (t0) REVERT: B 456 PHE cc_start: 0.9132 (m-80) cc_final: 0.8661 (m-80) REVERT: C 177 MET cc_start: -0.5139 (OUTLIER) cc_final: -0.5457 (ttt) REVERT: C 957 GLN cc_start: 0.8656 (tt0) cc_final: 0.8380 (tt0) REVERT: X 60 TYR cc_start: 0.4107 (m-80) cc_final: 0.3691 (m-80) REVERT: Y 64 VAL cc_start: 0.0668 (OUTLIER) cc_final: 0.0375 (p) REVERT: Y 83 MET cc_start: 0.1810 (mmp) cc_final: 0.0824 (mtp) outliers start: 30 outliers final: 19 residues processed: 111 average time/residue: 0.1613 time to fit residues: 31.7366 Evaluate side-chains 108 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 110 TYR Chi-restraints excluded: chain Z residue 5 VAL Chi-restraints excluded: chain Z residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 269 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 351 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 328 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 257 optimal weight: 30.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.151389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096359 restraints weight = 78103.527| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.45 r_work: 0.2950 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 29842 Z= 0.204 Angle : 0.646 20.320 40765 Z= 0.301 Chirality : 0.048 0.465 4745 Planarity : 0.003 0.051 5165 Dihedral : 8.561 105.242 5413 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.93 % Allowed : 11.63 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3562 helix: 2.28 (0.21), residues: 650 sheet: 0.29 (0.16), residues: 954 loop : -0.51 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.020 0.001 TYR C 265 PHE 0.015 0.001 PHE B 898 TRP 0.035 0.001 TRP C 152 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00480 (29725) covalent geometry : angle 0.59226 (40462) SS BOND : bond 0.00389 ( 42) SS BOND : angle 1.94589 ( 84) hydrogen bonds : bond 0.03897 ( 1162) hydrogen bonds : angle 5.20907 ( 3258) Misc. bond : bond 0.00078 ( 2) link_BETA1-4 : bond 0.00470 ( 19) link_BETA1-4 : angle 1.99942 ( 57) link_NAG-ASN : bond 0.00625 ( 54) link_NAG-ASN : angle 3.72516 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11014.97 seconds wall clock time: 188 minutes 21.43 seconds (11301.43 seconds total)