Starting phenix.real_space_refine on Mon Aug 25 11:08:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7akd_11812/08_2025/7akd_11812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7akd_11812/08_2025/7akd_11812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7akd_11812/08_2025/7akd_11812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7akd_11812/08_2025/7akd_11812.map" model { file = "/net/cci-nas-00/data/ceres_data/7akd_11812/08_2025/7akd_11812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7akd_11812/08_2025/7akd_11812.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 112 5.16 5 C 17403 2.51 5 N 4439 2.21 5 O 5404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27358 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 970, 7517 Classifications: {'peptide': 970} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 48, 'TRANS': 921} Chain breaks: 9 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 4, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7666 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 7 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 7685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7685 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 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: "X" 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: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 136 Unusual residues: {'FUC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 178 Unusual residues: {'FUC': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 108 Unusual residues: {'FUC': 1, 'NAG': 7} 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: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.98, per 1000 atoms: 0.26 Number of scatterers: 27358 At special positions: 0 Unit cell: (156.6, 143.64, 191.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 5404 8.00 N 4439 7.00 C 17403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 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 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " MAN T 4 " - " MAN T 5 " ALPHA1-6 " BMA T 3 " - " MAN T 4 " " MAN U 1 " - " MAN U 2 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG S 1 " - " FUC S 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 6 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1304 " - " ASN B 234 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1310 " - " ASN B 717 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1307 " - " ASN C 801 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 343 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN B 282 " " NAG O 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B1098 " " NAG S 1 " - " ASN C 282 " " NAG T 1 " - " ASN C 343 " " NAG W 1 " - " ASN C1074 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6352 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 57 sheets defined 24.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.421A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.003A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.087A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.614A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.513A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.570A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.899A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.521A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.873A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 945 Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.593A pdb=" N ASP A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.564A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.973A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.330A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.880A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.882A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.913A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.775A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.966A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.107A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.673A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.913A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.774A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 906 removed outlier: 3.878A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 910 removed outlier: 3.616A pdb=" N GLY B 910 " --> pdb=" O ASN B 907 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 907 through 910' Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.556A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.752A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.827A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.477A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.811A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.731A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.005A pdb=" N SER C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.352A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.146A 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: 3.671A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.540A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.313A 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: 3.657A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.713A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 4.040A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.753A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.685A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.767A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.533A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.114A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C1010 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.657A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.828A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.827A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.643A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.854A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.866A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.575A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.455A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.652A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.696A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.216A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.513A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.067A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.594A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.899A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.108A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.701A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE B 133 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B 114 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N CYS B 131 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER B 116 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS B 129 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU B 118 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL B 127 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.637A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.944A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.606A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 718 removed outlier: 6.477A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 721 through 728 removed outlier: 3.606A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.618A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.702A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.990A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.573A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.521A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.825A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.670A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.839A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.470A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 719 through 728 removed outlier: 3.681A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 719 through 728 removed outlier: 3.681A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.640A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.537A pdb=" N GLN D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.672A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.920A pdb=" N CYS D 95 " --> pdb=" O TRP D 111 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRP D 111 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG D 97 " --> pdb=" O GLU D 109 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.878A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.515A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.515A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.537A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.672A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.919A pdb=" N CYS H 95 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRP H 111 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG H 97 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.879A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.514A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.514A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2808 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: 7.57 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8594 1.35 - 1.47: 7398 1.47 - 1.60: 11826 1.60 - 1.72: 1 1.72 - 1.85: 140 Bond restraints: 27959 Sorted by residual: bond pdb=" C1 FUC T 6 " pdb=" C2 FUC T 6 " ideal model delta sigma weight residual 1.528 1.622 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 FUC T 6 " pdb=" O5 FUC T 6 " ideal model delta sigma weight residual 1.400 1.481 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1 MAN U 2 " pdb=" O5 MAN U 2 " ideal model delta sigma weight residual 1.399 1.450 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.569 -0.050 2.00e-02 2.50e+03 6.27e+00 bond pdb=" C1 MAN U 2 " pdb=" C2 MAN U 2 " ideal model delta sigma weight residual 1.526 1.576 -0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 27954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 37218 2.11 - 4.21: 740 4.21 - 6.32: 101 6.32 - 8.43: 13 8.43 - 10.53: 2 Bond angle restraints: 38074 Sorted by residual: angle pdb=" N VAL A 608 " pdb=" CA VAL A 608 " pdb=" CB VAL A 608 " ideal model delta sigma weight residual 112.32 104.67 7.65 1.15e+00 7.56e-01 4.42e+01 angle pdb=" N ASN A 606 " pdb=" CA ASN A 606 " pdb=" C ASN A 606 " ideal model delta sigma weight residual 110.06 117.00 -6.94 1.43e+00 4.89e-01 2.36e+01 angle pdb=" C ASN A 606 " pdb=" CA ASN A 606 " pdb=" CB ASN A 606 " ideal model delta sigma weight residual 111.97 102.93 9.04 1.99e+00 2.53e-01 2.06e+01 angle pdb=" N VAL C 608 " pdb=" CA VAL C 608 " pdb=" CB VAL C 608 " ideal model delta sigma weight residual 112.32 107.50 4.82 1.15e+00 7.56e-01 1.76e+01 angle pdb=" N ILE H 110 " pdb=" CA ILE H 110 " pdb=" CB ILE H 110 " ideal model delta sigma weight residual 111.41 116.96 -5.55 1.38e+00 5.25e-01 1.62e+01 ... (remaining 38069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.34: 16765 24.34 - 48.69: 578 48.69 - 73.03: 143 73.03 - 97.37: 67 97.37 - 121.72: 46 Dihedral angle restraints: 17599 sinusoidal: 7725 harmonic: 9874 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -149.74 63.74 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.90 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 147.14 -54.14 1 1.00e+01 1.00e-02 3.98e+01 ... (remaining 17596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 4511 0.144 - 0.287: 46 0.287 - 0.431: 8 0.431 - 0.575: 1 0.575 - 0.719: 1 Chirality restraints: 4567 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 4564 not shown) Planarity restraints: 4816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 714 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO C 715 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 715 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 715 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 760 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C CYS A 760 " 0.053 2.00e-02 2.50e+03 pdb=" O CYS A 760 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A 761 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C1059 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C GLY C1059 " -0.049 2.00e-02 2.50e+03 pdb=" O GLY C1059 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL C1060 " 0.016 2.00e-02 2.50e+03 ... (remaining 4813 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 440 2.68 - 3.24: 25814 3.24 - 3.79: 37203 3.79 - 4.35: 49724 4.35 - 4.90: 85238 Nonbonded interactions: 198419 Sorted by model distance: nonbonded pdb=" OD1 ASN B 360 " pdb=" OG1 THR B 523 " model vdw 2.126 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.138 3.040 nonbonded pdb=" OG SER C 708 " pdb=" OG SER C 711 " model vdw 2.141 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASN B 343 " pdb=" N2 NAG O 1 " model vdw 2.221 3.120 ... (remaining 198414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 82 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 109 or (res \ id 110 through 111 and (name N or name CA or name C or name O or name CB )) or r \ esid 112 through 113 or resid 116 through 128 or (resid 129 and (name N or name \ CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 thro \ ugh 138 and (name N or name CA or name C or name O or name CB )) or resid 139 th \ rough 140 or resid 166 through 172 or resid 187 through 241 or (resid 242 throug \ h 263 and (name N or name CA or name C or name O or name CB )) or resid 265 thro \ ugh 613 or (resid 614 and (name N or name CA or name C or name O or name CB )) o \ r resid 615 through 618 or (resid 619 and (name N or name CA or name C or name O \ or name CB )) or resid 620 through 676 or resid 690 through 827 or resid 856 th \ rough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 through 1305 or resid 1307)) selection = (chain 'B' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 110 or (resid 111 and (name N or name CA or name C or name O or nam \ e CB )) or resid 112 or (resid 113 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 134 or (resid 135 through 138 and (name N or na \ me CA or name C or name O or name CB )) or resid 139 through 140 or resid 166 th \ rough 196 or resid 200 through 385 or (resid 386 and (name N or name CA or name \ C or name O or name CB )) or resid 387 through 470 or resid 491 through 613 or ( \ resid 614 and (name N or name CA or name C or name O or name CB )) or resid 615 \ through 618 or (resid 619 and (name N or name CA or name C or name O or name CB \ )) or resid 620 through 920 or (resid 921 and (name N or name CA or name C or na \ me O or name CB )) or resid 922 through 1141 or (resid 1142 and (name N or name \ CA or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1147 through 13 \ 05 or resid 1307)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 through 109 or (resid 110 through 111 and (name N or name CA or name C or n \ ame O or name CB )) or resid 112 or (resid 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 123 or (resid 124 through 125 and ( \ name N or name CA or name C or name O or name CB )) or resid 126 through 131 or \ (resid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 \ or (resid 134 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 140 or resid 166 through 171 or (resid 172 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 196 or resid 2 \ 00 through 263 or resid 265 through 385 or (resid 386 and (name N or name CA or \ name C or name O or name CB )) or resid 387 through 470 or resid 491 through 827 \ or resid 856 through 1141 or (resid 1142 and (name N or name CA or name C or na \ me O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1147 through 1305 or \ resid 1307)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.470 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 0.094 28054 Z= 0.192 Angle : 0.776 16.218 38317 Z= 0.387 Chirality : 0.053 0.719 4567 Planarity : 0.005 0.103 4789 Dihedral : 15.682 121.719 11130 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.21 % Allowed : 4.26 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -1.66 (0.13), residues: 3342 helix: -1.82 (0.17), residues: 631 sheet: 0.17 (0.17), residues: 809 loop : -1.43 (0.12), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.003 ARG A 34 TYR 0.017 0.001 TYR B1067 PHE 0.020 0.001 PHE B 377 TRP 0.025 0.001 TRP B 104 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00372 (27959) covalent geometry : angle 0.71717 (38074) SS BOND : bond 0.00260 ( 39) SS BOND : angle 1.24796 ( 78) hydrogen bonds : bond 0.12990 ( 1029) hydrogen bonds : angle 6.99512 ( 2808) Misc. bond : bond 0.00009 ( 1) link_ALPHA1-3 : bond 0.00492 ( 2) link_ALPHA1-3 : angle 1.44432 ( 6) link_ALPHA1-6 : bond 0.00651 ( 2) link_ALPHA1-6 : angle 2.43713 ( 6) link_BETA1-4 : bond 0.00874 ( 22) link_BETA1-4 : angle 3.71222 ( 66) link_BETA1-6 : bond 0.03131 ( 2) link_BETA1-6 : angle 5.83380 ( 6) link_NAG-ASN : bond 0.00853 ( 27) link_NAG-ASN : angle 5.22724 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 479 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7589 (mt) cc_final: 0.7075 (pp) REVERT: A 754 LEU cc_start: 0.9044 (pp) cc_final: 0.8807 (tp) REVERT: A 948 LEU cc_start: 0.7921 (pp) cc_final: 0.7595 (pp) REVERT: A 974 SER cc_start: 0.9351 (t) cc_final: 0.8898 (m) REVERT: A 1002 GLN cc_start: 0.7684 (pt0) cc_final: 0.7137 (pt0) REVERT: B 338 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7309 (t80) REVERT: B 347 PHE cc_start: 0.5450 (t80) cc_final: 0.4994 (m-80) REVERT: B 753 LEU cc_start: 0.8700 (tt) cc_final: 0.8447 (tt) REVERT: C 338 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7807 (t80) REVERT: C 456 PHE cc_start: 0.8018 (m-80) cc_final: 0.7755 (m-80) REVERT: C 533 LEU cc_start: 0.8640 (mt) cc_final: 0.8192 (tt) REVERT: C 663 ASP cc_start: 0.7824 (t0) cc_final: 0.7513 (m-30) REVERT: E 35 TRP cc_start: 0.7788 (m100) cc_final: 0.7496 (m100) REVERT: H 58 ASN cc_start: 0.6211 (m-40) cc_final: 0.5899 (m-40) REVERT: L 58 ILE cc_start: 0.8140 (mm) cc_final: 0.7861 (mm) outliers start: 6 outliers final: 2 residues processed: 485 average time/residue: 0.1676 time to fit residues: 130.1107 Evaluate side-chains 243 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 239 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain C residue 338 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 271 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 314 GLN C 709 ASN L 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.161398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.125089 restraints weight = 41446.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127155 restraints weight = 101469.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128156 restraints weight = 55764.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127900 restraints weight = 45136.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129109 restraints weight = 33145.194| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28054 Z= 0.140 Angle : 0.721 16.882 38317 Z= 0.348 Chirality : 0.048 0.422 4567 Planarity : 0.004 0.051 4789 Dihedral : 11.854 119.074 5252 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.65 % Allowed : 8.83 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.67 (0.13), residues: 3342 helix: 0.02 (0.20), residues: 663 sheet: 0.50 (0.17), residues: 812 loop : -1.05 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 45 TYR 0.022 0.001 TYR B 91 PHE 0.030 0.002 PHE H 78 TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00300 (27959) covalent geometry : angle 0.66503 (38074) SS BOND : bond 0.00454 ( 39) SS BOND : angle 2.44457 ( 78) hydrogen bonds : bond 0.04567 ( 1029) hydrogen bonds : angle 5.70692 ( 2808) Misc. bond : bond 0.00105 ( 1) link_ALPHA1-3 : bond 0.00756 ( 2) link_ALPHA1-3 : angle 1.75834 ( 6) link_ALPHA1-6 : bond 0.01135 ( 2) link_ALPHA1-6 : angle 1.68211 ( 6) link_BETA1-4 : bond 0.01054 ( 22) link_BETA1-4 : angle 3.36266 ( 66) link_BETA1-6 : bond 0.03336 ( 2) link_BETA1-6 : angle 3.75306 ( 6) link_NAG-ASN : bond 0.00867 ( 27) link_NAG-ASN : angle 4.64352 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7527 (mt) cc_final: 0.7049 (pp) REVERT: A 606 ASN cc_start: 0.8154 (p0) cc_final: 0.7677 (p0) REVERT: A 692 ILE cc_start: 0.8696 (mt) cc_final: 0.8403 (mm) REVERT: A 974 SER cc_start: 0.9198 (t) cc_final: 0.8940 (m) REVERT: A 1002 GLN cc_start: 0.7575 (pt0) cc_final: 0.7245 (pt0) REVERT: B 201 PHE cc_start: 0.8034 (t80) cc_final: 0.7769 (t80) REVERT: B 338 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7327 (t80) REVERT: B 347 PHE cc_start: 0.5708 (t80) cc_final: 0.5307 (m-80) REVERT: C 338 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7636 (t80) REVERT: C 406 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7583 (mt-10) REVERT: C 429 PHE cc_start: 0.9402 (t80) cc_final: 0.9015 (t80) REVERT: C 453 TYR cc_start: 0.8382 (p90) cc_final: 0.8139 (p90) REVERT: C 533 LEU cc_start: 0.8626 (mt) cc_final: 0.8247 (tt) REVERT: C 663 ASP cc_start: 0.8011 (t0) cc_final: 0.7635 (m-30) REVERT: E 35 TRP cc_start: 0.7789 (m100) cc_final: 0.7378 (m100) REVERT: L 58 ILE cc_start: 0.8074 (mm) cc_final: 0.7829 (mm) outliers start: 48 outliers final: 30 residues processed: 311 average time/residue: 0.1715 time to fit residues: 87.9379 Evaluate side-chains 252 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 282 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 0.0040 chunk 187 optimal weight: 0.8980 chunk 298 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 127 optimal weight: 0.3980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN A1002 GLN B 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.162676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126082 restraints weight = 40964.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127094 restraints weight = 88256.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128697 restraints weight = 62701.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128514 restraints weight = 44483.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129831 restraints weight = 35871.548| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28054 Z= 0.115 Angle : 0.650 16.464 38317 Z= 0.308 Chirality : 0.046 0.386 4567 Planarity : 0.004 0.039 4789 Dihedral : 9.873 115.242 5252 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.13 % Allowed : 9.17 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.14), residues: 3342 helix: 0.90 (0.22), residues: 650 sheet: 0.66 (0.18), residues: 784 loop : -0.93 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1107 TYR 0.015 0.001 TYR A1067 PHE 0.024 0.001 PHE A 32 TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00237 (27959) covalent geometry : angle 0.60114 (38074) SS BOND : bond 0.00663 ( 39) SS BOND : angle 1.46147 ( 78) hydrogen bonds : bond 0.04041 ( 1029) hydrogen bonds : angle 5.26432 ( 2808) Misc. bond : bond 0.00125 ( 1) link_ALPHA1-3 : bond 0.00887 ( 2) link_ALPHA1-3 : angle 1.68970 ( 6) link_ALPHA1-6 : bond 0.01011 ( 2) link_ALPHA1-6 : angle 1.94635 ( 6) link_BETA1-4 : bond 0.00958 ( 22) link_BETA1-4 : angle 3.30040 ( 66) link_BETA1-6 : bond 0.02735 ( 2) link_BETA1-6 : angle 3.56224 ( 6) link_NAG-ASN : bond 0.00772 ( 27) link_NAG-ASN : angle 4.17274 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 250 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7524 (mt) cc_final: 0.6976 (pp) REVERT: A 606 ASN cc_start: 0.8175 (p0) cc_final: 0.7680 (p0) REVERT: A 754 LEU cc_start: 0.9095 (pp) cc_final: 0.8738 (tp) REVERT: A 974 SER cc_start: 0.9133 (t) cc_final: 0.8922 (m) REVERT: B 338 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7417 (t80) REVERT: B 347 PHE cc_start: 0.5763 (OUTLIER) cc_final: 0.5360 (m-80) REVERT: B 1139 ASP cc_start: 0.7369 (t0) cc_final: 0.7092 (t0) REVERT: C 338 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.7580 (t80) REVERT: C 403 ARG cc_start: 0.7377 (ttm170) cc_final: 0.7168 (ttm170) REVERT: C 453 TYR cc_start: 0.8411 (p90) cc_final: 0.8104 (p90) REVERT: C 533 LEU cc_start: 0.8567 (mt) cc_final: 0.8207 (tt) REVERT: C 663 ASP cc_start: 0.8023 (t0) cc_final: 0.7727 (m-30) REVERT: D 109 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7736 (tm-30) REVERT: H 18 LEU cc_start: 0.6857 (pp) cc_final: 0.6621 (pp) REVERT: H 60 ASN cc_start: 0.8153 (t0) cc_final: 0.7825 (t0) REVERT: L 46 LEU cc_start: 0.8442 (tp) cc_final: 0.8230 (tt) REVERT: L 47 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6634 (mt) REVERT: L 58 ILE cc_start: 0.8051 (mm) cc_final: 0.7771 (mm) REVERT: L 94 TRP cc_start: 0.6979 (t-100) cc_final: 0.6289 (t60) outliers start: 62 outliers final: 34 residues processed: 294 average time/residue: 0.1681 time to fit residues: 82.2289 Evaluate side-chains 254 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 196 optimal weight: 5.9990 chunk 257 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 129 optimal weight: 0.0870 chunk 99 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 394 ASN B1002 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.160476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123263 restraints weight = 40787.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124637 restraints weight = 90246.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125733 restraints weight = 63006.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125892 restraints weight = 42623.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127427 restraints weight = 33510.455| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28054 Z= 0.121 Angle : 0.638 15.357 38317 Z= 0.304 Chirality : 0.046 0.375 4567 Planarity : 0.004 0.060 4789 Dihedral : 8.840 110.300 5252 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.27 % Allowed : 9.96 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.16 (0.14), residues: 3342 helix: 1.05 (0.21), residues: 663 sheet: 0.83 (0.18), residues: 791 loop : -0.97 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 45 TYR 0.016 0.001 TYR C1067 PHE 0.021 0.001 PHE B 201 TRP 0.017 0.001 TRP B 436 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00262 (27959) covalent geometry : angle 0.59152 (38074) SS BOND : bond 0.00533 ( 39) SS BOND : angle 1.41292 ( 78) hydrogen bonds : bond 0.04140 ( 1029) hydrogen bonds : angle 5.11495 ( 2808) Misc. bond : bond 0.00110 ( 1) link_ALPHA1-3 : bond 0.00895 ( 2) link_ALPHA1-3 : angle 1.95627 ( 6) link_ALPHA1-6 : bond 0.01001 ( 2) link_ALPHA1-6 : angle 1.98946 ( 6) link_BETA1-4 : bond 0.00886 ( 22) link_BETA1-4 : angle 3.24960 ( 66) link_BETA1-6 : bond 0.02720 ( 2) link_BETA1-6 : angle 3.41248 ( 6) link_NAG-ASN : bond 0.00655 ( 27) link_NAG-ASN : angle 4.02887 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 238 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7481 (mt) cc_final: 0.6925 (pp) REVERT: A 675 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: A 754 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8730 (tp) REVERT: B 338 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7481 (t80) REVERT: B 347 PHE cc_start: 0.5730 (OUTLIER) cc_final: 0.5214 (m-80) REVERT: C 403 ARG cc_start: 0.7304 (ttm170) cc_final: 0.6290 (ttm-80) REVERT: C 421 TYR cc_start: 0.8268 (m-10) cc_final: 0.8055 (m-10) REVERT: C 453 TYR cc_start: 0.8509 (p90) cc_final: 0.8140 (p90) REVERT: C 533 LEU cc_start: 0.8614 (mt) cc_final: 0.8233 (tt) REVERT: D 109 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7765 (tm-30) REVERT: H 18 LEU cc_start: 0.7044 (pp) cc_final: 0.6813 (pp) REVERT: H 58 ASN cc_start: 0.7286 (t0) cc_final: 0.6747 (t0) REVERT: H 60 ASN cc_start: 0.8240 (t0) cc_final: 0.7772 (t0) REVERT: H 66 ARG cc_start: 0.6638 (mmm-85) cc_final: 0.6379 (mtp180) REVERT: L 46 LEU cc_start: 0.8478 (tp) cc_final: 0.8211 (tt) REVERT: L 47 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6659 (mt) REVERT: L 58 ILE cc_start: 0.8054 (mm) cc_final: 0.7807 (mm) REVERT: L 94 TRP cc_start: 0.6745 (t-100) cc_final: 0.5735 (t60) outliers start: 66 outliers final: 44 residues processed: 285 average time/residue: 0.1697 time to fit residues: 80.8504 Evaluate side-chains 260 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 50 optimal weight: 4.9990 chunk 197 optimal weight: 0.0070 chunk 259 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 220 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 274 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.158844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122394 restraints weight = 40676.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123399 restraints weight = 100407.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125178 restraints weight = 60983.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124946 restraints weight = 42257.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126372 restraints weight = 33475.316| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 28054 Z= 0.134 Angle : 0.643 14.825 38317 Z= 0.308 Chirality : 0.046 0.374 4567 Planarity : 0.004 0.060 4789 Dihedral : 8.295 105.550 5250 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.54 % Allowed : 10.71 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.12 (0.14), residues: 3342 helix: 1.17 (0.21), residues: 658 sheet: 0.88 (0.17), residues: 814 loop : -1.01 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 45 TYR 0.017 0.001 TYR C1067 PHE 0.021 0.002 PHE B 201 TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00305 (27959) covalent geometry : angle 0.59619 (38074) SS BOND : bond 0.00467 ( 39) SS BOND : angle 1.77201 ( 78) hydrogen bonds : bond 0.04420 ( 1029) hydrogen bonds : angle 5.08247 ( 2808) Misc. bond : bond 0.00110 ( 1) link_ALPHA1-3 : bond 0.00852 ( 2) link_ALPHA1-3 : angle 2.02614 ( 6) link_ALPHA1-6 : bond 0.01018 ( 2) link_ALPHA1-6 : angle 2.08653 ( 6) link_BETA1-4 : bond 0.00929 ( 22) link_BETA1-4 : angle 3.19917 ( 66) link_BETA1-6 : bond 0.02805 ( 2) link_BETA1-6 : angle 3.36403 ( 6) link_NAG-ASN : bond 0.00606 ( 27) link_NAG-ASN : angle 3.94581 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 222 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7777 (tmtt) REVERT: A 582 LEU cc_start: 0.7491 (mt) cc_final: 0.6933 (pp) REVERT: A 675 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: A 948 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7239 (pp) REVERT: B 338 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7517 (t80) REVERT: B 347 PHE cc_start: 0.5827 (OUTLIER) cc_final: 0.5265 (m-80) REVERT: C 406 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7026 (mp0) REVERT: C 420 ASP cc_start: 0.7834 (p0) cc_final: 0.7618 (p0) REVERT: C 453 TYR cc_start: 0.8533 (p90) cc_final: 0.8074 (p90) REVERT: C 533 LEU cc_start: 0.8641 (mt) cc_final: 0.8234 (tt) REVERT: D 109 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7749 (tm-30) REVERT: H 58 ASN cc_start: 0.7170 (t0) cc_final: 0.6735 (t0) REVERT: L 37 GLN cc_start: 0.7125 (tt0) cc_final: 0.6879 (tm-30) REVERT: L 46 LEU cc_start: 0.8458 (tp) cc_final: 0.8217 (tt) REVERT: L 47 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6607 (mt) REVERT: L 58 ILE cc_start: 0.8074 (mm) cc_final: 0.7829 (mm) REVERT: L 94 TRP cc_start: 0.6568 (t-100) cc_final: 0.5692 (t60) outliers start: 74 outliers final: 52 residues processed: 277 average time/residue: 0.1714 time to fit residues: 79.5835 Evaluate side-chains 261 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 102 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 0.0050 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN B 501 ASN B 655 HIS B 764 ASN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN L 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115289 restraints weight = 41184.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118226 restraints weight = 101954.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118574 restraints weight = 42863.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118707 restraints weight = 35176.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120033 restraints weight = 28008.552| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 28054 Z= 0.233 Angle : 0.757 14.933 38317 Z= 0.373 Chirality : 0.050 0.420 4567 Planarity : 0.005 0.069 4789 Dihedral : 8.338 96.441 5250 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.64 % Allowed : 11.40 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.59 (0.14), residues: 3342 helix: 0.65 (0.21), residues: 661 sheet: 0.66 (0.17), residues: 819 loop : -1.31 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 45 TYR 0.023 0.002 TYR C1067 PHE 0.028 0.003 PHE A1089 TRP 0.024 0.002 TRP C 64 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00568 (27959) covalent geometry : angle 0.71598 (38074) SS BOND : bond 0.00659 ( 39) SS BOND : angle 1.78922 ( 78) hydrogen bonds : bond 0.06210 ( 1029) hydrogen bonds : angle 5.46553 ( 2808) Misc. bond : bond 0.00102 ( 1) link_ALPHA1-3 : bond 0.00791 ( 2) link_ALPHA1-3 : angle 2.14235 ( 6) link_ALPHA1-6 : bond 0.01017 ( 2) link_ALPHA1-6 : angle 2.14184 ( 6) link_BETA1-4 : bond 0.00877 ( 22) link_BETA1-4 : angle 3.14215 ( 66) link_BETA1-6 : bond 0.02082 ( 2) link_BETA1-6 : angle 3.10027 ( 6) link_NAG-ASN : bond 0.00570 ( 27) link_NAG-ASN : angle 4.19647 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 218 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8302 (m-80) cc_final: 0.8058 (m-80) REVERT: A 214 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8017 (ptp-170) REVERT: A 582 LEU cc_start: 0.7697 (mt) cc_final: 0.6988 (pp) REVERT: A 900 MET cc_start: 0.8108 (mtt) cc_final: 0.7658 (mtt) REVERT: A 1127 ASP cc_start: 0.8240 (t0) cc_final: 0.7881 (t0) REVERT: B 338 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7737 (t80) REVERT: B 347 PHE cc_start: 0.6354 (t80) cc_final: 0.5346 (m-80) REVERT: C 453 TYR cc_start: 0.8567 (p90) cc_final: 0.8151 (p90) REVERT: C 533 LEU cc_start: 0.8743 (mt) cc_final: 0.8306 (tt) REVERT: C 900 MET cc_start: 0.8090 (mmm) cc_final: 0.7615 (mtt) REVERT: D 95 CYS cc_start: 0.5221 (p) cc_final: 0.4721 (p) REVERT: D 108 PHE cc_start: 0.7729 (m-80) cc_final: 0.7471 (m-80) REVERT: D 109 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7792 (tm-30) REVERT: E 35 TRP cc_start: 0.7549 (m100) cc_final: 0.7235 (m100) REVERT: H 58 ASN cc_start: 0.7250 (t0) cc_final: 0.6550 (t0) REVERT: L 37 GLN cc_start: 0.7302 (tt0) cc_final: 0.6953 (tm-30) REVERT: L 47 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6970 (mt) REVERT: L 58 ILE cc_start: 0.8061 (mm) cc_final: 0.7841 (mm) REVERT: L 94 TRP cc_start: 0.6726 (t-100) cc_final: 0.6517 (t-100) outliers start: 77 outliers final: 60 residues processed: 276 average time/residue: 0.1778 time to fit residues: 81.6044 Evaluate side-chains 268 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 26 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 196 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN H 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.154921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117183 restraints weight = 40704.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118328 restraints weight = 98521.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119649 restraints weight = 60709.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120828 restraints weight = 36370.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121547 restraints weight = 31153.996| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28054 Z= 0.131 Angle : 0.662 14.588 38317 Z= 0.318 Chirality : 0.046 0.357 4567 Planarity : 0.004 0.059 4789 Dihedral : 7.865 90.461 5247 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.47 % Allowed : 12.23 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.38 (0.14), residues: 3342 helix: 1.09 (0.21), residues: 649 sheet: 0.62 (0.17), residues: 827 loop : -1.20 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.019 0.001 TYR A1138 PHE 0.022 0.001 PHE B 201 TRP 0.016 0.001 TRP B 436 HIS 0.002 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00292 (27959) covalent geometry : angle 0.61794 (38074) SS BOND : bond 0.00404 ( 39) SS BOND : angle 1.54380 ( 78) hydrogen bonds : bond 0.04863 ( 1029) hydrogen bonds : angle 5.13749 ( 2808) Misc. bond : bond 0.00100 ( 1) link_ALPHA1-3 : bond 0.00793 ( 2) link_ALPHA1-3 : angle 2.08263 ( 6) link_ALPHA1-6 : bond 0.01003 ( 2) link_ALPHA1-6 : angle 2.18796 ( 6) link_BETA1-4 : bond 0.00917 ( 22) link_BETA1-4 : angle 3.15417 ( 66) link_BETA1-6 : bond 0.02627 ( 2) link_BETA1-6 : angle 3.29605 ( 6) link_NAG-ASN : bond 0.00608 ( 27) link_NAG-ASN : angle 4.01093 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 212 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8100 (m-80) cc_final: 0.7846 (m-80) REVERT: A 582 LEU cc_start: 0.7722 (mt) cc_final: 0.7048 (pp) REVERT: A 979 ASP cc_start: 0.8269 (t0) cc_final: 0.8038 (t0) REVERT: B 338 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7764 (t80) REVERT: B 347 PHE cc_start: 0.6126 (t80) cc_final: 0.5162 (m-80) REVERT: C 453 TYR cc_start: 0.8531 (p90) cc_final: 0.8091 (p90) REVERT: C 533 LEU cc_start: 0.8700 (mt) cc_final: 0.8248 (tt) REVERT: C 584 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8515 (pt) REVERT: C 900 MET cc_start: 0.8052 (mmm) cc_final: 0.7669 (mtt) REVERT: D 95 CYS cc_start: 0.5247 (p) cc_final: 0.4678 (p) REVERT: D 108 PHE cc_start: 0.7634 (m-80) cc_final: 0.7321 (m-80) REVERT: D 109 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7780 (tm-30) REVERT: E 35 TRP cc_start: 0.7513 (m100) cc_final: 0.7210 (m100) REVERT: H 58 ASN cc_start: 0.7246 (t0) cc_final: 0.6535 (t0) REVERT: L 37 GLN cc_start: 0.7305 (tt0) cc_final: 0.6949 (tm-30) REVERT: L 47 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6854 (mt) REVERT: L 58 ILE cc_start: 0.8031 (mm) cc_final: 0.7797 (mm) REVERT: L 94 TRP cc_start: 0.6530 (t-100) cc_final: 0.6306 (t-100) outliers start: 72 outliers final: 55 residues processed: 270 average time/residue: 0.1702 time to fit residues: 77.2026 Evaluate side-chains 257 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 138 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 319 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN ** B 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN E 92 ASN H 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114839 restraints weight = 41501.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116275 restraints weight = 104646.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117797 restraints weight = 57365.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118309 restraints weight = 36475.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119455 restraints weight = 30779.958| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28054 Z= 0.183 Angle : 0.700 14.833 38317 Z= 0.340 Chirality : 0.048 0.385 4567 Planarity : 0.005 0.060 4789 Dihedral : 7.839 80.547 5247 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.47 % Allowed : 12.43 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.62 (0.14), residues: 3342 helix: 0.86 (0.21), residues: 649 sheet: 0.52 (0.18), residues: 823 loop : -1.35 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.025 0.002 TYR C 200 PHE 0.025 0.002 PHE A1121 TRP 0.021 0.001 TRP C 64 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00437 (27959) covalent geometry : angle 0.65823 (38074) SS BOND : bond 0.00536 ( 39) SS BOND : angle 1.60008 ( 78) hydrogen bonds : bond 0.05584 ( 1029) hydrogen bonds : angle 5.25261 ( 2808) Misc. bond : bond 0.00097 ( 1) link_ALPHA1-3 : bond 0.00760 ( 2) link_ALPHA1-3 : angle 2.09774 ( 6) link_ALPHA1-6 : bond 0.00997 ( 2) link_ALPHA1-6 : angle 2.09214 ( 6) link_BETA1-4 : bond 0.00874 ( 22) link_BETA1-4 : angle 3.12434 ( 66) link_BETA1-6 : bond 0.02568 ( 2) link_BETA1-6 : angle 3.10690 ( 6) link_NAG-ASN : bond 0.00545 ( 27) link_NAG-ASN : angle 4.02846 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 210 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7746 (mt) cc_final: 0.7024 (pp) REVERT: A 900 MET cc_start: 0.8123 (mtt) cc_final: 0.7706 (mtt) REVERT: A 1127 ASP cc_start: 0.8237 (t0) cc_final: 0.7714 (t0) REVERT: B 338 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7766 (t80) REVERT: B 347 PHE cc_start: 0.6369 (t80) cc_final: 0.5283 (m-80) REVERT: C 453 TYR cc_start: 0.8574 (p90) cc_final: 0.8150 (p90) REVERT: C 533 LEU cc_start: 0.8732 (mt) cc_final: 0.8256 (tt) REVERT: C 584 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8570 (pt) REVERT: C 900 MET cc_start: 0.8087 (mmm) cc_final: 0.7635 (mtt) REVERT: D 95 CYS cc_start: 0.5326 (p) cc_final: 0.4753 (p) REVERT: D 99 VAL cc_start: 0.9510 (p) cc_final: 0.9290 (m) REVERT: D 108 PHE cc_start: 0.7668 (m-80) cc_final: 0.7343 (m-80) REVERT: D 109 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7795 (tm-30) REVERT: E 35 TRP cc_start: 0.7567 (m100) cc_final: 0.7273 (m100) REVERT: H 58 ASN cc_start: 0.7223 (t0) cc_final: 0.6538 (t0) REVERT: L 35 TRP cc_start: 0.8194 (m100) cc_final: 0.7935 (m100) REVERT: L 37 GLN cc_start: 0.7316 (tt0) cc_final: 0.6926 (tm-30) REVERT: L 47 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6926 (mt) REVERT: L 58 ILE cc_start: 0.8084 (mm) cc_final: 0.7868 (mm) REVERT: L 94 TRP cc_start: 0.6615 (t-100) cc_final: 0.6375 (t-100) outliers start: 72 outliers final: 55 residues processed: 268 average time/residue: 0.1720 time to fit residues: 77.0676 Evaluate side-chains 259 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 30 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 245 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 298 optimal weight: 0.8980 chunk 324 optimal weight: 8.9990 chunk 162 optimal weight: 0.0980 chunk 278 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN E 92 ASN H 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118002 restraints weight = 41047.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118949 restraints weight = 98513.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120992 restraints weight = 60987.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120894 restraints weight = 40763.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122296 restraints weight = 32729.725| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28054 Z= 0.118 Angle : 0.650 14.339 38317 Z= 0.309 Chirality : 0.046 0.346 4567 Planarity : 0.004 0.048 4789 Dihedral : 7.430 71.945 5247 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.92 % Allowed : 13.36 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.37 (0.14), residues: 3342 helix: 1.25 (0.22), residues: 649 sheet: 0.59 (0.18), residues: 843 loop : -1.24 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.016 0.001 TYR A1067 PHE 0.024 0.001 PHE B 201 TRP 0.014 0.001 TRP B 436 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00254 (27959) covalent geometry : angle 0.60530 (38074) SS BOND : bond 0.00372 ( 39) SS BOND : angle 1.84852 ( 78) hydrogen bonds : bond 0.04458 ( 1029) hydrogen bonds : angle 5.02343 ( 2808) Misc. bond : bond 0.00093 ( 1) link_ALPHA1-3 : bond 0.00777 ( 2) link_ALPHA1-3 : angle 2.02489 ( 6) link_ALPHA1-6 : bond 0.00987 ( 2) link_ALPHA1-6 : angle 2.08854 ( 6) link_BETA1-4 : bond 0.00900 ( 22) link_BETA1-4 : angle 3.14889 ( 66) link_BETA1-6 : bond 0.02646 ( 2) link_BETA1-6 : angle 3.24718 ( 6) link_NAG-ASN : bond 0.00609 ( 27) link_NAG-ASN : angle 3.82853 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7651 (mt) cc_final: 0.7001 (pp) REVERT: A 1127 ASP cc_start: 0.8224 (t0) cc_final: 0.7721 (t0) REVERT: B 338 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7794 (t80) REVERT: B 347 PHE cc_start: 0.6150 (t80) cc_final: 0.5101 (m-80) REVERT: C 453 TYR cc_start: 0.8570 (p90) cc_final: 0.8089 (p90) REVERT: C 533 LEU cc_start: 0.8738 (mt) cc_final: 0.8274 (tt) REVERT: C 568 ASP cc_start: 0.6407 (m-30) cc_final: 0.5913 (p0) REVERT: C 584 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8533 (pt) REVERT: C 900 MET cc_start: 0.7970 (mmm) cc_final: 0.7589 (mtt) REVERT: D 95 CYS cc_start: 0.5426 (p) cc_final: 0.4841 (p) REVERT: D 99 VAL cc_start: 0.9448 (p) cc_final: 0.9217 (m) REVERT: D 109 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7793 (tm-30) REVERT: E 35 TRP cc_start: 0.7529 (m100) cc_final: 0.7221 (m100) REVERT: H 58 ASN cc_start: 0.7419 (t0) cc_final: 0.6668 (t0) REVERT: L 35 TRP cc_start: 0.8183 (m100) cc_final: 0.7954 (m100) REVERT: L 37 GLN cc_start: 0.7209 (tt0) cc_final: 0.6850 (tm-30) REVERT: L 47 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6666 (mt) REVERT: L 94 TRP cc_start: 0.6539 (t-100) cc_final: 0.6337 (t-100) outliers start: 56 outliers final: 48 residues processed: 255 average time/residue: 0.1623 time to fit residues: 69.4390 Evaluate side-chains 256 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 243 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 327 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN E 92 ASN H 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118778 restraints weight = 41508.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121517 restraints weight = 99629.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121242 restraints weight = 42696.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121827 restraints weight = 33392.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122182 restraints weight = 28170.928| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 28054 Z= 0.149 Angle : 0.673 14.911 38317 Z= 0.322 Chirality : 0.046 0.358 4567 Planarity : 0.004 0.045 4789 Dihedral : 7.351 61.223 5247 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.92 % Allowed : 13.39 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.47 (0.14), residues: 3342 helix: 1.14 (0.21), residues: 649 sheet: 0.54 (0.18), residues: 820 loop : -1.29 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 237 TYR 0.021 0.001 TYR C 421 PHE 0.024 0.002 PHE B 201 TRP 0.014 0.001 TRP C 64 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00349 (27959) covalent geometry : angle 0.63108 (38074) SS BOND : bond 0.00433 ( 39) SS BOND : angle 1.76084 ( 78) hydrogen bonds : bond 0.04932 ( 1029) hydrogen bonds : angle 5.08870 ( 2808) Misc. bond : bond 0.00094 ( 1) link_ALPHA1-3 : bond 0.00741 ( 2) link_ALPHA1-3 : angle 2.01001 ( 6) link_ALPHA1-6 : bond 0.00993 ( 2) link_ALPHA1-6 : angle 2.02219 ( 6) link_BETA1-4 : bond 0.00848 ( 22) link_BETA1-4 : angle 3.11595 ( 66) link_BETA1-6 : bond 0.02446 ( 2) link_BETA1-6 : angle 3.06179 ( 6) link_NAG-ASN : bond 0.00524 ( 27) link_NAG-ASN : angle 3.87732 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7587 (mt) cc_final: 0.6919 (pp) REVERT: B 338 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7813 (t80) REVERT: B 347 PHE cc_start: 0.6153 (t80) cc_final: 0.5090 (m-80) REVERT: C 453 TYR cc_start: 0.8519 (p90) cc_final: 0.8118 (p90) REVERT: C 533 LEU cc_start: 0.8710 (mt) cc_final: 0.8247 (tt) REVERT: C 568 ASP cc_start: 0.6442 (m-30) cc_final: 0.6015 (p0) REVERT: C 584 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8552 (pt) REVERT: C 900 MET cc_start: 0.8043 (mmm) cc_final: 0.7576 (mtt) REVERT: D 95 CYS cc_start: 0.5413 (p) cc_final: 0.4857 (p) REVERT: D 99 VAL cc_start: 0.9503 (p) cc_final: 0.9262 (m) REVERT: D 109 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7757 (tm-30) REVERT: E 35 TRP cc_start: 0.7538 (m100) cc_final: 0.7247 (m100) REVERT: E 42 GLN cc_start: 0.6162 (mm-40) cc_final: 0.5899 (mm-40) REVERT: H 58 ASN cc_start: 0.7431 (t0) cc_final: 0.6683 (t0) REVERT: L 35 TRP cc_start: 0.8274 (m100) cc_final: 0.8038 (m100) REVERT: L 37 GLN cc_start: 0.7246 (tt0) cc_final: 0.6938 (tm-30) REVERT: L 47 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6875 (mt) REVERT: L 94 TRP cc_start: 0.6475 (t-100) cc_final: 0.6251 (t-100) outliers start: 56 outliers final: 51 residues processed: 256 average time/residue: 0.1638 time to fit residues: 70.4099 Evaluate side-chains 261 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 134 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 chunk 264 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 274 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 73 optimal weight: 0.0270 chunk 299 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN E 92 ASN H 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118525 restraints weight = 41104.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121351 restraints weight = 100747.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121171 restraints weight = 42409.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121632 restraints weight = 33344.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122081 restraints weight = 28041.597| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28054 Z= 0.142 Angle : 0.777 59.197 38317 Z= 0.397 Chirality : 0.047 0.518 4567 Planarity : 0.004 0.056 4789 Dihedral : 7.347 61.029 5247 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.92 % Allowed : 13.43 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 aren not related in a simple way. whole: -0.47 (0.14), residues: 3342 helix: 1.16 (0.21), residues: 649 sheet: 0.54 (0.18), residues: 820 loop : -1.29 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 237 TYR 0.017 0.001 TYR C1067 PHE 0.023 0.001 PHE B 201 TRP 0.014 0.001 TRP B 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00313 (27959) covalent geometry : angle 0.74136 (38074) SS BOND : bond 0.00408 ( 39) SS BOND : angle 1.73875 ( 78) hydrogen bonds : bond 0.04877 ( 1029) hydrogen bonds : angle 5.08366 ( 2808) Misc. bond : bond 0.00095 ( 1) link_ALPHA1-3 : bond 0.00746 ( 2) link_ALPHA1-3 : angle 2.00534 ( 6) link_ALPHA1-6 : bond 0.00993 ( 2) link_ALPHA1-6 : angle 2.02086 ( 6) link_BETA1-4 : bond 0.00848 ( 22) link_BETA1-4 : angle 3.11364 ( 66) link_BETA1-6 : bond 0.02440 ( 2) link_BETA1-6 : angle 3.13755 ( 6) link_NAG-ASN : bond 0.00525 ( 27) link_NAG-ASN : angle 3.86936 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3722.52 seconds wall clock time: 65 minutes 39.45 seconds (3939.45 seconds total)