Starting phenix.real_space_refine on Mon Sep 14 11:33:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cak_30333/09_2026/7cak_30333.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cak_30333/09_2026/7cak_30333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cak_30333/09_2026/7cak_30333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cak_30333/09_2026/7cak_30333.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cak_30333/09_2026/7cak_30333.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cak_30333/09_2026/7cak_30333.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cak_30333/09_2026/7cak_30333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cak_30333/09_2026/7cak_30333.cif" } resolution = 3.58 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 129 5.16 5 C 19264 2.51 5 N 4934 2.21 5 O 5936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30263 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8029 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 50, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8033 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8033 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 837 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 837 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 837 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 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 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 chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.71, per 1000 atoms: 0.22 Number of scatterers: 30263 At special positions: 0 Unit cell: (174.72, 165.36, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5936 8.00 N 4934 7.00 C 19264 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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 480 " - pdb=" SG CYS C 488 " 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=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 87 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 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 Atom "HETATM30205 O5 NAG C1306 .*. O " rejected from bonding due to valence issues. Atom "HETATM30093 O5 NAG B1308 .*. O " rejected from bonding due to valence issues. Atom "HETATM30233 O5 NAG C1308 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7068 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 75 sheets defined 18.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.792A pdb=" N PHE A 157 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.895A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.556A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.833A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.682A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.307A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.723A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 901 Processing helix chain 'A' and resid 903 through 908 removed outlier: 3.621A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.638A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.529A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (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: 3.968A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.568A pdb=" N ALA A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.791A pdb=" N PHE B 157 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.895A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.556A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.834A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.683A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.307A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.640A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.723A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 901 Processing helix chain 'B' and resid 903 through 908 removed outlier: 3.622A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.640A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.528A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (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 removed outlier: 3.968A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.567A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B1023 " --> pdb=" O ARG B1019 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 157 removed outlier: 3.791A pdb=" N PHE C 157 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.895A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.556A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.834A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.682A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.308A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.722A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 901 Processing helix chain 'C' and resid 903 through 908 removed outlier: 3.621A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.639A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.529A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (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 removed outlier: 3.968A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.568A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.596A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.631A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.519A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 90 Processing sheet with id=AA6, first strand: chain 'A' and resid 89 through 90 removed outlier: 7.110A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.323A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.421A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.178A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.672A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 576 through 577 Processing sheet with id=AB7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.883A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.557A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 725 through 728 removed outlier: 7.034A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC2, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.597A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.631A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.520A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AC8, first strand: chain 'B' and resid 89 through 90 removed outlier: 7.110A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.323A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.422A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AD3, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.178A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.882A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.557A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 725 through 728 removed outlier: 7.034A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE4, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AE5, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AE6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.596A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.631A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.520A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AF2, first strand: chain 'C' and resid 89 through 90 removed outlier: 7.111A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.322A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.422A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AF6, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.179A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AF9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AG2, first strand: chain 'C' and resid 576 through 577 Processing sheet with id=AG3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.884A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.557A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 725 through 728 removed outlier: 7.035A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AG7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AG8, first strand: chain 'C' and resid 1095 through 1097 Processing sheet with id=AG9, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.512A pdb=" N GLN D 10 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.553A pdb=" N THR E 69 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.587A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AH5, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.338A pdb=" N GLN F 10 " --> pdb=" O GLU F 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'F' and resid 44 through 47 removed outlier: 6.086A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AH8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.524A pdb=" N ILE G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR G 50 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AI1, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.511A pdb=" N GLN H 10 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.553A pdb=" N THR I 69 " --> pdb=" O GLU I 82 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.588A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) 895 hydrogen bonds defined for protein. 2319 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: 8.12 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6661 1.32 - 1.45: 9162 1.45 - 1.57: 14965 1.57 - 1.70: 3 1.70 - 1.83: 159 Bond restraints: 30950 Sorted by residual: bond pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 1.331 1.456 -0.125 1.24e-02 6.50e+03 1.02e+02 bond pdb=" C LEU C 335 " pdb=" N CYS C 336 " ideal model delta sigma weight residual 1.331 1.455 -0.125 1.24e-02 6.50e+03 1.01e+02 bond pdb=" C LEU B 335 " pdb=" N CYS B 336 " ideal model delta sigma weight residual 1.331 1.455 -0.124 1.24e-02 6.50e+03 1.00e+02 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.21e+01 bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.502 -0.168 2.34e-02 1.83e+03 5.18e+01 ... (remaining 30945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 40147 3.50 - 7.00: 1658 7.00 - 10.50: 202 10.50 - 14.00: 72 14.00 - 17.50: 21 Bond angle restraints: 42100 Sorted by residual: angle pdb=" C LYS A 733 " pdb=" N THR A 734 " pdb=" CA THR A 734 " ideal model delta sigma weight residual 122.73 108.74 13.99 1.92e+00 2.71e-01 5.31e+01 angle pdb=" C LYS C 733 " pdb=" N THR C 734 " pdb=" CA THR C 734 " ideal model delta sigma weight residual 122.73 108.79 13.94 1.92e+00 2.71e-01 5.27e+01 angle pdb=" C LYS B 733 " pdb=" N THR B 734 " pdb=" CA THR B 734 " ideal model delta sigma weight residual 122.73 108.80 13.93 1.92e+00 2.71e-01 5.26e+01 angle pdb=" C HIS A1088 " pdb=" N PHE A1089 " pdb=" CA PHE A1089 " ideal model delta sigma weight residual 123.56 110.05 13.51 1.98e+00 2.55e-01 4.66e+01 angle pdb=" C HIS B1088 " pdb=" N PHE B1089 " pdb=" CA PHE B1089 " ideal model delta sigma weight residual 123.56 110.06 13.50 1.98e+00 2.55e-01 4.65e+01 ... (remaining 42095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 16719 17.13 - 34.25: 1004 34.25 - 51.38: 108 51.38 - 68.51: 55 68.51 - 85.63: 18 Dihedral angle restraints: 17904 sinusoidal: 6915 harmonic: 10989 Sorted by residual: dihedral pdb=" CA TRP F 93 " pdb=" C TRP F 93 " pdb=" N PRO F 94 " pdb=" CA PRO F 94 " ideal model delta harmonic sigma weight residual -180.00 -129.50 -50.50 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA TRP D 93 " pdb=" C TRP D 93 " pdb=" N PRO D 94 " pdb=" CA PRO D 94 " ideal model delta harmonic sigma weight residual 180.00 -132.83 -47.17 0 5.00e+00 4.00e-02 8.90e+01 dihedral pdb=" CA TRP H 93 " pdb=" C TRP H 93 " pdb=" N PRO H 94 " pdb=" CA PRO H 94 " ideal model delta harmonic sigma weight residual -180.00 -132.84 -47.16 0 5.00e+00 4.00e-02 8.90e+01 ... (remaining 17901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.332: 4908 0.332 - 0.664: 16 0.664 - 0.996: 4 0.996 - 1.328: 0 1.328 - 1.660: 1 Chirality restraints: 4929 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-01 2.50e+01 6.89e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.36e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.34e+01 ... (remaining 4926 not shown) Planarity restraints: 5387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.062 2.00e-02 2.50e+03 6.09e-02 4.63e+01 pdb=" CG ASN A 603 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP D 93 " 0.099 5.00e-02 4.00e+02 1.50e-01 3.60e+01 pdb=" N PRO D 94 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO D 94 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO D 94 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP H 93 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO H 94 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO H 94 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO H 94 " -0.075 5.00e-02 4.00e+02 ... (remaining 5384 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.85: 8 1.85 - 2.61: 1567 2.61 - 3.37: 43921 3.37 - 4.14: 77509 4.14 - 4.90: 135927 Nonbonded interactions: 258932 Sorted by model distance: nonbonded pdb=" OE2 GLU B 324 " pdb=" O SER B 325 " model vdw 1.082 3.040 nonbonded pdb=" O ASN A 856 " pdb=" CD1 LEU A 858 " model vdw 1.222 3.460 nonbonded pdb=" O PHE C 855 " pdb=" ND2 ASN C 856 " model vdw 1.310 3.120 nonbonded pdb=" CZ PHE A 559 " pdb=" O PHE A 565 " model vdw 1.367 3.340 nonbonded pdb=" CB ARG A 408 " pdb=" OD1 ASP E 102 " model vdw 1.433 3.440 ... (remaining 258927 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' selection = (chain 'B' and (resid 25 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1310)) selection = (chain 'C' and (resid 25 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 29.800 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 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 : 0.027 0.196 31049 Z= 1.232 Angle : 1.728 34.089 42358 Z= 0.897 Chirality : 0.093 1.660 4929 Planarity : 0.009 0.150 5342 Dihedral : 11.562 83.546 10719 Min Nonbonded Distance : 1.082 Molprobity Statistics. All-atom Clashscore : 48.79 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.40 % Favored : 89.79 % Rotamer: Outliers : 1.80 % Allowed : 2.23 % Favored : 95.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.10), residues: 3711 helix: -5.11 (0.06), residues: 621 sheet: -2.67 (0.13), residues: 918 loop : -2.87 (0.11), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 44 TYR 0.055 0.005 TYR F 95 PHE 0.070 0.006 PHE C1042 TRP 0.048 0.007 TRP B 64 HIS 0.022 0.005 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.02737 / 1.23 (30950) covalent geometry : angle 1.66528 / 0.89 (42100) SS BOND : bond 0.00864 / 0.61 ( 39) SS BOND : angle 1.74929 / 1.19 ( 78) hydrogen bonds : bond 0.32039 / 21.00 ( 871) hydrogen bonds : angle 12.37826 / 8.47 ( 2319) link_BETA1-4 : bond 0.01386 / 0.79 ( 15) link_BETA1-4 : angle 3.94873 / 2.75 ( 45) link_NAG-ASN : bond 0.02327 / 1.44 ( 45) link_NAG-ASN : angle 8.08215 / 4.88 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 182 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8548 (m-80) REVERT: A 850 ILE cc_start: 0.3066 (OUTLIER) cc_final: 0.2518 (mp) REVERT: A 853 GLN cc_start: 0.3906 (OUTLIER) cc_final: 0.3580 (mt0) REVERT: A 1089 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8717 (m-10) REVERT: A 1113 GLN cc_start: 0.7784 (mt0) cc_final: 0.7406 (mt0) REVERT: B 864 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8026 (tp) REVERT: C 858 LEU cc_start: 0.8441 (mp) cc_final: 0.8224 (mt) REVERT: C 902 MET cc_start: 0.8927 (mmm) cc_final: 0.8649 (mmm) REVERT: C 1113 GLN cc_start: 0.7859 (mt0) cc_final: 0.7576 (mt0) REVERT: G 6 GLN cc_start: 0.3204 (mt0) cc_final: 0.2110 (tt0) outliers start: 59 outliers final: 35 residues processed: 239 average time/residue: 0.2028 time to fit residues: 77.3730 Evaluate side-chains 127 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 414 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 66 HIS B 354 ASN B 437 ASN B 580 GLN B 655 HIS ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 66 HIS C 218 GLN C 354 ASN C 437 ASN C 580 GLN C 655 HIS ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN D 99 GLN F 10 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN I 6 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.146650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.102144 restraints weight = 78074.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100000 restraints weight = 70744.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.099660 restraints weight = 64157.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.100032 restraints weight = 62558.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100580 restraints weight = 50310.503| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 31049 Z= 0.237 Angle : 0.885 14.482 42358 Z= 0.454 Chirality : 0.053 0.502 4929 Planarity : 0.006 0.138 5342 Dihedral : 8.761 86.020 4113 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.28 % Favored : 94.50 % Rotamer: Outliers : 1.95 % Allowed : 5.13 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.12), residues: 3711 helix: -2.78 (0.14), residues: 639 sheet: -2.16 (0.14), residues: 942 loop : -2.07 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 214 TYR 0.044 0.002 TYR H 95 PHE 0.027 0.002 PHE E 54 TRP 0.048 0.003 TRP H 93 HIS 0.011 0.002 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 (30950) covalent geometry : angle 0.84682 / 0.45 (42100) SS BOND : bond 0.00592 / 0.36 ( 39) SS BOND : angle 1.92904 / 1.22 ( 78) hydrogen bonds : bond 0.06093 / 4.06 ( 871) hydrogen bonds : angle 7.61576 / 5.31 ( 2319) link_BETA1-4 : bond 0.00478 / 0.31 ( 15) link_BETA1-4 : angle 1.84037 / 1.20 ( 45) link_NAG-ASN : bond 0.00515 / 0.31 ( 45) link_NAG-ASN : angle 4.32045 / 2.87 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.6916 (m-80) cc_final: 0.6682 (m-80) REVERT: A 1050 MET cc_start: 0.8742 (ptm) cc_final: 0.8519 (ptm) REVERT: B 564 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7452 (tp40) REVERT: B 740 MET cc_start: 0.7359 (tpt) cc_final: 0.7033 (tpt) REVERT: B 864 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8269 (tp) REVERT: D 31 ASN cc_start: 0.2896 (t0) cc_final: 0.2144 (m110) REVERT: G 6 GLN cc_start: 0.4519 (mt0) cc_final: 0.3514 (tt0) REVERT: G 110 TRP cc_start: 0.2285 (OUTLIER) cc_final: 0.1752 (m-90) outliers start: 64 outliers final: 33 residues processed: 221 average time/residue: 0.1778 time to fit residues: 65.5987 Evaluate side-chains 130 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 292 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 247 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 205 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 308 optimal weight: 50.0000 chunk 268 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 414 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1119 ASN B 134 GLN B 354 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 134 GLN C 354 ASN C 437 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1119 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN E 6 GLN ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN G 6 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.144472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.099983 restraints weight = 75199.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097260 restraints weight = 53790.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096608 restraints weight = 57763.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096608 restraints weight = 51520.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096608 restraints weight = 51520.699| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 31049 Z= 0.159 Angle : 0.731 12.582 42358 Z= 0.372 Chirality : 0.048 0.450 4929 Planarity : 0.005 0.123 5342 Dihedral : 7.175 76.074 4067 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.17 % Favored : 94.66 % Rotamer: Outliers : 1.92 % Allowed : 6.28 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.13), residues: 3711 helix: -0.69 (0.20), residues: 636 sheet: -1.69 (0.15), residues: 933 loop : -1.57 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 158 TYR 0.031 0.002 TYR H 95 PHE 0.028 0.002 PHE E 54 TRP 0.072 0.002 TRP H 93 HIS 0.007 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (30950) covalent geometry : angle 0.70060 / 0.36 (42100) SS BOND : bond 0.00231 / 0.15 ( 39) SS BOND : angle 2.35785 / 1.46 ( 78) hydrogen bonds : bond 0.04395 / 2.93 ( 871) hydrogen bonds : angle 6.61347 / 4.63 ( 2319) link_BETA1-4 : bond 0.00381 / 0.27 ( 15) link_BETA1-4 : angle 1.36635 / 0.92 ( 45) link_NAG-ASN : bond 0.00463 / 0.29 ( 45) link_NAG-ASN : angle 3.30781 / 2.22 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 143 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.7056 (m-80) cc_final: 0.6673 (m-80) REVERT: A 739 THR cc_start: 0.8914 (m) cc_final: 0.8637 (p) REVERT: A 906 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: B 1050 MET cc_start: 0.8642 (ptm) cc_final: 0.8111 (ptm) REVERT: C 739 THR cc_start: 0.8919 (m) cc_final: 0.8650 (p) REVERT: D 31 ASN cc_start: 0.2625 (t0) cc_final: 0.2089 (m110) REVERT: F 43 PRO cc_start: 0.4590 (Cg_exo) cc_final: 0.3990 (Cg_endo) REVERT: G 6 GLN cc_start: 0.4668 (mt0) cc_final: 0.4155 (tt0) REVERT: G 110 TRP cc_start: 0.1960 (OUTLIER) cc_final: 0.1742 (m-90) REVERT: I 107 MET cc_start: 0.0573 (ptp) cc_final: 0.0316 (ptp) REVERT: I 110 TRP cc_start: 0.1870 (m-10) cc_final: 0.1571 (m-10) outliers start: 63 outliers final: 28 residues processed: 197 average time/residue: 0.1658 time to fit residues: 56.1681 Evaluate side-chains 128 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 33 HIS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 104 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 195 optimal weight: 0.5980 chunk 203 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 327 optimal weight: 50.0000 chunk 148 optimal weight: 9.9990 chunk 35 optimal weight: 40.0000 chunk 314 optimal weight: 30.0000 chunk 226 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.144536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.098736 restraints weight = 79213.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.097988 restraints weight = 64126.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.098327 restraints weight = 52429.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.098205 restraints weight = 47090.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.098205 restraints weight = 49942.518| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31049 Z= 0.262 Angle : 0.743 11.538 42358 Z= 0.373 Chirality : 0.049 0.422 4929 Planarity : 0.005 0.121 5342 Dihedral : 6.555 75.416 4053 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.01 % Favored : 93.83 % Rotamer: Outliers : 2.14 % Allowed : 7.50 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.13), residues: 3711 helix: -0.31 (0.20), residues: 657 sheet: -1.74 (0.15), residues: 969 loop : -1.57 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 158 TYR 0.021 0.002 TYR G 50 PHE 0.024 0.002 PHE E 54 TRP 0.028 0.002 TRP G 110 HIS 0.009 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.26 (30950) covalent geometry : angle 0.71653 / 0.37 (42100) SS BOND : bond 0.00348 / 0.20 ( 39) SS BOND : angle 1.78474 / 1.44 ( 78) hydrogen bonds : bond 0.04246 / 2.80 ( 871) hydrogen bonds : angle 6.45239 / 4.51 ( 2319) link_BETA1-4 : bond 0.00167 / 0.11 ( 15) link_BETA1-4 : angle 1.56208 / 1.14 ( 45) link_NAG-ASN : bond 0.00564 / 0.35 ( 45) link_NAG-ASN : angle 3.23380 / 2.18 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 107 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: C 563 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7032 (mm110) REVERT: C 761 THR cc_start: 0.8430 (p) cc_final: 0.8204 (t) REVERT: C 957 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8219 (tm-30) REVERT: E 23 LYS cc_start: 0.4262 (OUTLIER) cc_final: 0.3746 (mmmm) REVERT: F 43 PRO cc_start: 0.4280 (Cg_exo) cc_final: 0.3995 (Cg_endo) REVERT: G 6 GLN cc_start: 0.4987 (mt0) cc_final: 0.4202 (tp-100) REVERT: G 110 TRP cc_start: 0.2794 (OUTLIER) cc_final: 0.2225 (m-90) REVERT: I 107 MET cc_start: 0.0671 (ptp) cc_final: 0.0438 (ptp) outliers start: 70 outliers final: 50 residues processed: 170 average time/residue: 0.1576 time to fit residues: 47.3756 Evaluate side-chains 142 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 88 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 33 HIS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 104 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 363 optimal weight: 30.0000 chunk 185 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 chunk 362 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN B 935 GLN C1005 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.144776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.101865 restraints weight = 75501.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099424 restraints weight = 61999.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.098985 restraints weight = 54057.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.099486 restraints weight = 46879.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099401 restraints weight = 43977.765| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 31049 Z= 0.210 Angle : 0.677 11.303 42358 Z= 0.343 Chirality : 0.047 0.424 4929 Planarity : 0.004 0.105 5342 Dihedral : 6.108 80.683 4049 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.55 % Favored : 94.29 % Rotamer: Outliers : 2.10 % Allowed : 8.48 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.13), residues: 3711 helix: 0.05 (0.21), residues: 657 sheet: -1.55 (0.16), residues: 948 loop : -1.51 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.019 0.002 TYR G 50 PHE 0.025 0.002 PHE B 133 TRP 0.029 0.002 TRP G 110 HIS 0.006 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (30950) covalent geometry : angle 0.65032 / 0.34 (42100) SS BOND : bond 0.00242 / 0.16 ( 39) SS BOND : angle 1.72210 / 1.38 ( 78) hydrogen bonds : bond 0.03894 / 2.58 ( 871) hydrogen bonds : angle 6.17547 / 4.33 ( 2319) link_BETA1-4 : bond 0.00258 / 0.19 ( 15) link_BETA1-4 : angle 1.35911 / 0.94 ( 45) link_NAG-ASN : bond 0.00476 / 0.29 ( 45) link_NAG-ASN : angle 3.11043 / 2.09 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 105 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: B 1050 MET cc_start: 0.8335 (ptm) cc_final: 0.7806 (ptm) REVERT: C 957 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8053 (tm-30) REVERT: E 23 LYS cc_start: 0.4147 (OUTLIER) cc_final: 0.3646 (mmmm) REVERT: E 80 TYR cc_start: 0.4804 (OUTLIER) cc_final: 0.4437 (t80) REVERT: F 43 PRO cc_start: 0.4369 (Cg_exo) cc_final: 0.4013 (Cg_endo) REVERT: G 6 GLN cc_start: 0.4959 (mt0) cc_final: 0.4345 (tp-100) REVERT: I 110 TRP cc_start: 0.2155 (m-10) cc_final: 0.1645 (m-10) outliers start: 69 outliers final: 46 residues processed: 166 average time/residue: 0.1573 time to fit residues: 46.4904 Evaluate side-chains 140 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 91 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 33 HIS Chi-restraints excluded: chain D residue 93 TRP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 104 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 180 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 256 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 0.0020 chunk 339 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 580 GLN C 580 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.145622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099389 restraints weight = 76935.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098976 restraints weight = 65727.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099352 restraints weight = 49354.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099189 restraints weight = 46272.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099758 restraints weight = 46513.737| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31049 Z= 0.139 Angle : 0.628 11.099 42358 Z= 0.318 Chirality : 0.046 0.406 4929 Planarity : 0.004 0.100 5342 Dihedral : 5.483 44.648 4042 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.83 % Rotamer: Outliers : 1.62 % Allowed : 9.64 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3711 helix: 0.43 (0.21), residues: 657 sheet: -1.35 (0.16), residues: 948 loop : -1.41 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.015 0.001 TYR B1067 PHE 0.022 0.001 PHE E 54 TRP 0.061 0.002 TRP G 110 HIS 0.006 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (30950) covalent geometry : angle 0.60229 / 0.31 (42100) SS BOND : bond 0.00244 / 0.18 ( 39) SS BOND : angle 1.56757 / 1.26 ( 78) hydrogen bonds : bond 0.03593 / 2.40 ( 871) hydrogen bonds : angle 5.86850 / 4.13 ( 2319) link_BETA1-4 : bond 0.00289 / 0.21 ( 15) link_BETA1-4 : angle 1.24973 / 0.85 ( 45) link_NAG-ASN : bond 0.00440 / 0.27 ( 45) link_NAG-ASN : angle 2.94217 / 1.98 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 104 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8836 (tt) cc_final: 0.8165 (mp) REVERT: A 900 MET cc_start: 0.7769 (ttm) cc_final: 0.7555 (ttp) REVERT: A 906 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8564 (m-80) REVERT: B 902 MET cc_start: 0.8812 (mmm) cc_final: 0.8519 (mmm) REVERT: B 1050 MET cc_start: 0.8393 (ptm) cc_final: 0.7913 (ptm) REVERT: C 118 LEU cc_start: 0.8860 (tt) cc_final: 0.8231 (mp) REVERT: C 957 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7956 (tm-30) REVERT: E 80 TYR cc_start: 0.4419 (OUTLIER) cc_final: 0.3813 (t80) REVERT: G 6 GLN cc_start: 0.4513 (mt0) cc_final: 0.4110 (tp-100) REVERT: I 107 MET cc_start: 0.0630 (ptp) cc_final: 0.0213 (ptp) REVERT: I 110 TRP cc_start: 0.1783 (m-10) cc_final: 0.0961 (m-10) outliers start: 53 outliers final: 40 residues processed: 152 average time/residue: 0.1560 time to fit residues: 42.2370 Evaluate side-chains 130 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 88 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 33 HIS Chi-restraints excluded: chain D residue 93 TRP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 104 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 139 optimal weight: 50.0000 chunk 121 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 344 optimal weight: 20.0000 chunk 179 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1119 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1119 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.145235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.102514 restraints weight = 80747.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.099230 restraints weight = 55172.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.099488 restraints weight = 62275.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.099985 restraints weight = 53681.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100688 restraints weight = 46605.167| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 31049 Z= 0.374 Angle : 0.764 10.243 42358 Z= 0.384 Chirality : 0.050 0.396 4929 Planarity : 0.005 0.096 5342 Dihedral : 5.786 43.740 4042 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.44 % Favored : 93.42 % Rotamer: Outliers : 2.20 % Allowed : 9.67 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.13), residues: 3711 helix: -0.05 (0.20), residues: 663 sheet: -1.47 (0.16), residues: 987 loop : -1.68 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 905 TYR 0.020 0.002 TYR B1067 PHE 0.023 0.002 PHE B 133 TRP 0.063 0.003 TRP G 110 HIS 0.008 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.37 (30950) covalent geometry : angle 0.73864 / 0.38 (42100) SS BOND : bond 0.00336 / 0.22 ( 39) SS BOND : angle 1.98785 / 1.59 ( 78) hydrogen bonds : bond 0.04123 / 2.74 ( 871) hydrogen bonds : angle 6.23815 / 4.36 ( 2319) link_BETA1-4 : bond 0.00193 / 0.12 ( 15) link_BETA1-4 : angle 1.65693 / 1.23 ( 45) link_NAG-ASN : bond 0.00661 / 0.40 ( 45) link_NAG-ASN : angle 3.13699 / 2.12 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 89 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8877 (m-80) REVERT: C 761 THR cc_start: 0.8645 (p) cc_final: 0.8260 (t) REVERT: C 869 MET cc_start: 0.7951 (mtp) cc_final: 0.7677 (mtp) REVERT: C 957 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8042 (tm-30) REVERT: C 1029 MET cc_start: 0.9006 (tpp) cc_final: 0.8799 (tpp) REVERT: E 80 TYR cc_start: 0.4228 (OUTLIER) cc_final: 0.3820 (t80) REVERT: G 6 GLN cc_start: 0.5025 (mt0) cc_final: 0.4396 (tp40) REVERT: H 44 LYS cc_start: 0.7154 (mttp) cc_final: 0.6925 (mptt) REVERT: I 107 MET cc_start: 0.0331 (ptp) cc_final: -0.0118 (ptp) REVERT: I 110 TRP cc_start: 0.1949 (m-10) cc_final: 0.1356 (m-10) outliers start: 72 outliers final: 59 residues processed: 154 average time/residue: 0.1477 time to fit residues: 41.0269 Evaluate side-chains 144 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 83 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 33 HIS Chi-restraints excluded: chain D residue 93 TRP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 104 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 304 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 306 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 139 optimal weight: 50.0000 chunk 215 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.144335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101213 restraints weight = 80386.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098234 restraints weight = 60991.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098123 restraints weight = 58804.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098434 restraints weight = 57875.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098719 restraints weight = 46760.468| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 31049 Z= 0.369 Angle : 0.780 12.074 42358 Z= 0.391 Chirality : 0.050 0.395 4929 Planarity : 0.005 0.094 5342 Dihedral : 5.903 41.404 4042 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.82 % Favored : 93.05 % Rotamer: Outliers : 2.23 % Allowed : 9.76 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.13), residues: 3711 helix: -0.26 (0.20), residues: 663 sheet: -1.54 (0.16), residues: 981 loop : -1.82 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 214 TYR 0.023 0.002 TYR B1067 PHE 0.024 0.002 PHE B 133 TRP 0.071 0.003 TRP G 110 HIS 0.011 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.37 (30950) covalent geometry : angle 0.75551 / 0.39 (42100) SS BOND : bond 0.00341 / 0.23 ( 39) SS BOND : angle 2.02769 / 1.61 ( 78) hydrogen bonds : bond 0.04139 / 2.75 ( 871) hydrogen bonds : angle 6.38345 / 4.46 ( 2319) link_BETA1-4 : bond 0.00197 / 0.12 ( 15) link_BETA1-4 : angle 1.64761 / 1.19 ( 45) link_NAG-ASN : bond 0.00635 / 0.39 ( 45) link_NAG-ASN : angle 3.12941 / 2.12 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 86 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: C 761 THR cc_start: 0.8715 (p) cc_final: 0.8363 (t) REVERT: C 869 MET cc_start: 0.7925 (mtp) cc_final: 0.7667 (mtp) REVERT: C 957 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8103 (tm-30) REVERT: E 80 TYR cc_start: 0.3917 (OUTLIER) cc_final: 0.3627 (t80) REVERT: G 6 GLN cc_start: 0.5140 (mt0) cc_final: 0.3795 (tt0) outliers start: 73 outliers final: 64 residues processed: 152 average time/residue: 0.1495 time to fit residues: 40.6760 Evaluate side-chains 151 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 85 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 33 HIS Chi-restraints excluded: chain D residue 93 TRP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 104 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 185 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 332 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1011 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.144759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.099187 restraints weight = 77845.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.098910 restraints weight = 68642.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.099247 restraints weight = 53291.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.099697 restraints weight = 45558.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.099982 restraints weight = 42124.628| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31049 Z= 0.168 Angle : 0.654 10.408 42358 Z= 0.330 Chirality : 0.046 0.393 4929 Planarity : 0.004 0.097 5342 Dihedral : 5.473 32.149 4042 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 1.68 % Allowed : 10.37 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 3711 helix: 0.16 (0.21), residues: 663 sheet: -1.28 (0.17), residues: 945 loop : -1.64 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1019 TYR 0.020 0.001 TYR H 95 PHE 0.024 0.001 PHE E 54 TRP 0.057 0.002 TRP G 110 HIS 0.011 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (30950) covalent geometry : angle 0.63070 / 0.32 (42100) SS BOND : bond 0.00223 / 0.14 ( 39) SS BOND : angle 1.67024 / 1.32 ( 78) hydrogen bonds : bond 0.03654 / 2.42 ( 871) hydrogen bonds : angle 6.01845 / 4.23 ( 2319) link_BETA1-4 : bond 0.00198 / 0.14 ( 15) link_BETA1-4 : angle 1.34456 / 0.93 ( 45) link_NAG-ASN : bond 0.00439 / 0.27 ( 45) link_NAG-ASN : angle 2.85098 / 1.92 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 92 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8568 (m-80) REVERT: C 761 THR cc_start: 0.8553 (p) cc_final: 0.8169 (t) REVERT: C 869 MET cc_start: 0.7688 (mtp) cc_final: 0.7448 (mtp) REVERT: C 957 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7858 (tm-30) REVERT: C 1029 MET cc_start: 0.8723 (tpp) cc_final: 0.8450 (ttm) REVERT: E 80 TYR cc_start: 0.4182 (OUTLIER) cc_final: 0.3651 (t80) REVERT: G 6 GLN cc_start: 0.4736 (mt0) cc_final: 0.3264 (tt0) outliers start: 55 outliers final: 48 residues processed: 142 average time/residue: 0.1477 time to fit residues: 37.3880 Evaluate side-chains 135 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 85 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 33 HIS Chi-restraints excluded: chain D residue 93 TRP Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 139 optimal weight: 8.9990 chunk 208 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 349 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 367 optimal weight: 20.0000 chunk 109 optimal weight: 0.4980 chunk 357 optimal weight: 0.5980 chunk 233 optimal weight: 0.0870 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN C 580 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.143359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096263 restraints weight = 73855.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094797 restraints weight = 55353.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.093935 restraints weight = 52148.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.094416 restraints weight = 56520.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094777 restraints weight = 46996.772| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31049 Z= 0.146 Angle : 0.629 10.340 42358 Z= 0.316 Chirality : 0.046 0.391 4929 Planarity : 0.004 0.086 5342 Dihedral : 5.188 23.860 4040 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.25 % Favored : 94.61 % Rotamer: Outliers : 1.56 % Allowed : 10.71 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.14), residues: 3711 helix: 0.45 (0.21), residues: 663 sheet: -1.09 (0.17), residues: 936 loop : -1.51 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1019 TYR 0.017 0.001 TYR F 85 PHE 0.024 0.001 PHE E 54 TRP 0.054 0.002 TRP G 110 HIS 0.009 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (30950) covalent geometry : angle 0.60675 / 0.31 (42100) SS BOND : bond 0.00223 / 0.14 ( 39) SS BOND : angle 1.44643 / 1.18 ( 78) hydrogen bonds : bond 0.03518 / 2.33 ( 871) hydrogen bonds : angle 5.81214 / 4.08 ( 2319) link_BETA1-4 : bond 0.00228 / 0.16 ( 15) link_BETA1-4 : angle 1.27994 / 0.92 ( 45) link_NAG-ASN : bond 0.00430 / 0.27 ( 45) link_NAG-ASN : angle 2.73751 / 1.85 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 88 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.7808 (mtt) cc_final: 0.7570 (mtt) REVERT: A 906 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8577 (m-80) REVERT: B 855 PHE cc_start: 0.7704 (m-10) cc_final: 0.7209 (m-10) REVERT: C 869 MET cc_start: 0.7665 (mtp) cc_final: 0.7418 (mtp) REVERT: C 957 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8095 (tm-30) REVERT: E 80 TYR cc_start: 0.4244 (OUTLIER) cc_final: 0.3706 (t80) REVERT: E 81 MET cc_start: 0.1277 (mmp) cc_final: 0.0446 (tpp) REVERT: G 6 GLN cc_start: 0.4899 (mt0) cc_final: 0.3603 (tt0) outliers start: 51 outliers final: 42 residues processed: 133 average time/residue: 0.1593 time to fit residues: 37.2900 Evaluate side-chains 126 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 82 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 33 HIS Chi-restraints excluded: chain D residue 93 TRP Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 266 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 333 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 142 optimal weight: 50.0000 chunk 47 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 287 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 901 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.145825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.102507 restraints weight = 80161.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101512 restraints weight = 57852.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.101153 restraints weight = 48257.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101489 restraints weight = 48284.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101837 restraints weight = 44284.378| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31049 Z= 0.136 Angle : 0.610 10.136 42358 Z= 0.307 Chirality : 0.045 0.382 4929 Planarity : 0.004 0.084 5342 Dihedral : 5.000 24.454 4040 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.69 % Rotamer: Outliers : 1.49 % Allowed : 10.74 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3711 helix: 0.64 (0.21), residues: 663 sheet: -0.94 (0.17), residues: 972 loop : -1.43 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.017 0.001 TYR E 33 PHE 0.025 0.001 PHE E 54 TRP 0.049 0.002 TRP G 110 HIS 0.010 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (30950) covalent geometry : angle 0.59001 / 0.30 (42100) SS BOND : bond 0.00208 / 0.13 ( 39) SS BOND : angle 1.33116 / 1.12 ( 78) hydrogen bonds : bond 0.03399 / 2.26 ( 871) hydrogen bonds : angle 5.62875 / 3.95 ( 2319) link_BETA1-4 : bond 0.00236 / 0.16 ( 15) link_BETA1-4 : angle 1.21314 / 0.85 ( 45) link_NAG-ASN : bond 0.00418 / 0.26 ( 45) link_NAG-ASN : angle 2.61184 / 1.76 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4672.72 seconds wall clock time: 82 minutes 31.43 seconds (4951.43 seconds total)