Starting phenix.real_space_refine on Fri Mar 6 10:43:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws3_32742/03_2026/7ws3_32742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws3_32742/03_2026/7ws3_32742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws3_32742/03_2026/7ws3_32742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws3_32742/03_2026/7ws3_32742.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws3_32742/03_2026/7ws3_32742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws3_32742/03_2026/7ws3_32742.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 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 138 5.16 5 C 19191 2.51 5 N 4966 2.21 5 O 5920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30215 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8063 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 7 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 8048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8048 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8053 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 52, 'TRANS': 986} Chain breaks: 7 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.65, per 1000 atoms: 0.22 Number of scatterers: 30215 At special positions: 0 Unit cell: (150.06, 136.12, 210.74, 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 138 16.00 O 5920 8.00 N 4966 7.00 C 19191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN A 343 " " 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 343 " " 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: 2.64 Conformation dependent library (CDL) restraints added in 1.5 seconds 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7106 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 73 sheets defined 21.6% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.517A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.593A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.702A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.855A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.524A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.562A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.976A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.542A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.158A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.847A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.124A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.268A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.953A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.707A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.046A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.707A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.728A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.955A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.668A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.973A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.416A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.666A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.310A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.847A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.735A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.754A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.725A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.902A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.965A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 891 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.833A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.310A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.772A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.298A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.019A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.986A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.818A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.987A pdb=" N ASP G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.988A pdb=" N ASP I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.363A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.799A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.218A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.218A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.509A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.529A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.602A pdb=" N ASP A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 156 " --> pdb=" O ASP A 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.055A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.996A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.853A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.703A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.694A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.512A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.571A pdb=" N PHE A1052 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.433A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.522A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.574A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 132 through 142 removed outlier: 4.291A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP B 138 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLY B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE B 140 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLU B 156 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.198A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.956A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.546A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.828A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.354A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.508A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.585A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.891A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.548A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.521A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.655A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.427A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 133 through 135 removed outlier: 4.248A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.333A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.238A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.266A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.554A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.553A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.553A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 4.664A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF8, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.710A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AG1, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.922A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.744A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.677A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR E 112 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.677A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR E 94 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.708A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AG8, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.923A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.744A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AH2, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR G 112 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR G 94 " --> pdb=" O THR G 117 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.711A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AH6, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.923A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR H 98 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.745A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AH9, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.678A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR I 112 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.678A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR I 94 " --> pdb=" O THR I 117 " (cutoff:3.500A) 1153 hydrogen bonds defined for protein. 3138 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: 8.54 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8061 1.33 - 1.46: 8462 1.46 - 1.59: 14189 1.59 - 1.71: 0 1.71 - 1.84: 177 Bond restraints: 30889 Sorted by residual: bond pdb=" N THR E 106 " pdb=" CA THR E 106 " ideal model delta sigma weight residual 1.453 1.487 -0.033 9.20e-03 1.18e+04 1.32e+01 bond pdb=" C PRO B 986 " pdb=" O PRO B 986 " ideal model delta sigma weight residual 1.240 1.205 0.035 1.12e-02 7.97e+03 9.91e+00 bond pdb=" N GLU E 103 " pdb=" CA GLU E 103 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.44e+00 bond pdb=" C ASP B 985 " pdb=" N PRO B 986 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.32e+00 bond pdb=" N ARG H 18 " pdb=" CA ARG H 18 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.20e-02 6.94e+03 8.17e+00 ... (remaining 30884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 41402 2.34 - 4.68: 577 4.68 - 7.02: 50 7.02 - 9.37: 10 9.37 - 11.71: 1 Bond angle restraints: 42040 Sorted by residual: angle pdb=" CA PRO B 986 " pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 117.93 123.20 -5.27 1.20e+00 6.94e-01 1.93e+01 angle pdb=" CB ARG C 452 " pdb=" CG ARG C 452 " pdb=" CD ARG C 452 " ideal model delta sigma weight residual 111.30 119.62 -8.32 2.30e+00 1.89e-01 1.31e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.98 -4.28 1.22e+00 6.72e-01 1.23e+01 angle pdb=" CB LYS C 814 " pdb=" CG LYS C 814 " pdb=" CD LYS C 814 " ideal model delta sigma weight residual 111.30 119.06 -7.76 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA LEU B 461 " pdb=" CB LEU B 461 " pdb=" CG LEU B 461 " ideal model delta sigma weight residual 116.30 128.01 -11.71 3.50e+00 8.16e-02 1.12e+01 ... (remaining 42035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 17391 17.86 - 35.72: 1293 35.72 - 53.57: 283 53.57 - 71.43: 47 71.43 - 89.29: 27 Dihedral angle restraints: 19041 sinusoidal: 7984 harmonic: 11057 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.05 -88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -174.94 88.94 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -171.66 85.66 1 1.00e+01 1.00e-02 8.87e+01 ... (remaining 19038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4882 0.140 - 0.280: 20 0.280 - 0.419: 1 0.419 - 0.559: 2 0.559 - 0.699: 1 Chirality restraints: 4906 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.62e+00 ... (remaining 4903 not shown) Planarity restraints: 5416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 874 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C THR C 874 " 0.057 2.00e-02 2.50e+03 pdb=" O THR C 874 " -0.021 2.00e-02 2.50e+03 pdb=" N SER C 875 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.053 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO A 337 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.58e+00 pdb=" N PRO C 337 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.039 5.00e-02 4.00e+02 ... (remaining 5413 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2296 2.74 - 3.28: 28655 3.28 - 3.82: 46722 3.82 - 4.36: 54176 4.36 - 4.90: 97237 Nonbonded interactions: 229086 Sorted by model distance: nonbonded pdb=" NH2 ARG A 403 " pdb=" OD2 ASP A 405 " model vdw 2.202 3.120 nonbonded pdb=" ND2 ASN A 439 " pdb=" OH TYR D 32 " model vdw 2.207 3.120 nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.233 3.120 nonbonded pdb=" NH1 ARG F 61 " pdb=" OD2 ASP F 82 " model vdw 2.258 3.120 nonbonded pdb=" NH1 ARG H 61 " pdb=" OD2 ASP H 82 " model vdw 2.258 3.120 ... (remaining 229081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 108 or (resid 109 through 110 and (name N or na \ me CA or name C or name O or name CB )) or resid 111 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 or (resid 5 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 557 through \ 827 or resid 854 through 984 or (resid 985 and (name N or name CA or name C or \ name O or name CB )) or resid 986 through 1044 or (resid 1045 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1046 through 1307)) selection = (chain 'B' and (resid 15 through 555 or (resid 556 and (name N or name CA or nam \ e C or name O or name CB )) or resid 557 or (resid 558 through 559 and (name N o \ r name CA or name C or name O or name CB )) or resid 560 through 785 or (resid 7 \ 86 and (name N or name CA or name C or name O or name CB )) or resid 787 through \ 827 or (resid 854 and (name N or name CA or name C or name O or name CB )) or r \ esid 855 through 903 or (resid 904 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ ) \ ) or resid 905 through 1044 or (resid 1045 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1046 through 1307)) selection = (chain 'C' and (resid 15 through 108 or (resid 109 through 110 and (name N or na \ me CA or name C or name O or name CB )) or resid 111 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 557 \ or (resid 558 through 559 and (name N or name CA or name C or name O or name CB \ )) or resid 560 through 827 or resid 854 through 903 or (resid 904 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or resid 905 through 984 or (resid 985 and (n \ ame N or name CA or name C or name O or name CB )) or resid 986 through 1307)) } 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: 11.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.430 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30986 Z= 0.193 Angle : 0.669 12.697 42288 Z= 0.341 Chirality : 0.048 0.699 4906 Planarity : 0.004 0.082 5377 Dihedral : 13.163 89.288 11806 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3751 helix: 0.98 (0.21), residues: 673 sheet: -0.34 (0.16), residues: 1049 loop : -1.32 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 452 TYR 0.022 0.001 TYR B 453 PHE 0.019 0.001 PHE A 490 TRP 0.016 0.001 TRP A 258 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00364 (30889) covalent geometry : angle 0.64725 (42040) SS BOND : bond 0.00312 ( 43) SS BOND : angle 1.32852 ( 86) hydrogen bonds : bond 0.23364 ( 1091) hydrogen bonds : angle 8.52833 ( 3138) link_BETA1-4 : bond 0.00432 ( 15) link_BETA1-4 : angle 1.75360 ( 45) link_NAG-ASN : bond 0.00356 ( 39) link_NAG-ASN : angle 2.93835 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 ILE cc_start: 0.5834 (pt) cc_final: 0.5341 (pt) REVERT: F 4 MET cc_start: 0.5234 (mmm) cc_final: 0.4764 (tpp) outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.1868 time to fit residues: 129.7729 Evaluate side-chains 250 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 580 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 422 ASN C 580 GLN C 762 GLN C 774 GLN D 34 ASN D 37 GLN D 89 GLN F 6 GLN F 27 GLN F 34 ASN F 37 GLN F 89 GLN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.109042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.074189 restraints weight = 75670.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076935 restraints weight = 43824.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.078774 restraints weight = 31377.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.079912 restraints weight = 25346.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.080713 restraints weight = 22096.447| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30986 Z= 0.184 Angle : 0.644 12.224 42288 Z= 0.330 Chirality : 0.047 0.464 4906 Planarity : 0.004 0.057 5377 Dihedral : 6.654 59.549 5220 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.20 % Allowed : 7.16 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 3751 helix: 1.40 (0.21), residues: 667 sheet: -0.29 (0.16), residues: 1089 loop : -1.41 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 452 TYR 0.028 0.002 TYR C1067 PHE 0.026 0.002 PHE A 238 TRP 0.012 0.001 TRP I 113 HIS 0.005 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00435 (30889) covalent geometry : angle 0.62524 (42040) SS BOND : bond 0.00520 ( 43) SS BOND : angle 1.50883 ( 86) hydrogen bonds : bond 0.05451 ( 1091) hydrogen bonds : angle 6.13821 ( 3138) link_BETA1-4 : bond 0.00375 ( 15) link_BETA1-4 : angle 1.28709 ( 45) link_NAG-ASN : bond 0.00330 ( 39) link_NAG-ASN : angle 2.64687 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 LEU cc_start: 0.8499 (mm) cc_final: 0.8262 (mp) REVERT: B 452 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7960 (mmm-85) REVERT: D 37 GLN cc_start: 0.7682 (tm130) cc_final: 0.7420 (tm-30) REVERT: D 70 ASP cc_start: 0.7693 (t0) cc_final: 0.7163 (t70) REVERT: E 31 ASP cc_start: 0.8359 (t0) cc_final: 0.8096 (t0) REVERT: E 89 GLU cc_start: 0.8066 (pm20) cc_final: 0.7861 (pm20) REVERT: F 4 MET cc_start: 0.6612 (mmm) cc_final: 0.6050 (mmm) REVERT: F 92 TYR cc_start: 0.6792 (t80) cc_final: 0.6091 (t80) REVERT: G 112 TYR cc_start: 0.8071 (t80) cc_final: 0.7519 (t80) REVERT: H 79 GLN cc_start: 0.8253 (mm110) cc_final: 0.7658 (mp10) REVERT: I 28 THR cc_start: 0.9048 (t) cc_final: 0.8582 (p) outliers start: 39 outliers final: 21 residues processed: 297 average time/residue: 0.1944 time to fit residues: 93.6224 Evaluate side-chains 257 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 113 TRP Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 0 optimal weight: 30.0000 chunk 166 optimal weight: 3.9990 chunk 322 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 320 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 374 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN H 34 ASN H 37 GLN H 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.108121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.073582 restraints weight = 75581.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076345 restraints weight = 43950.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078172 restraints weight = 31508.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079359 restraints weight = 25431.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.080107 restraints weight = 22099.545| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30986 Z= 0.219 Angle : 0.640 12.291 42288 Z= 0.328 Chirality : 0.046 0.441 4906 Planarity : 0.004 0.056 5377 Dihedral : 6.134 54.164 5220 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.39 % Allowed : 10.59 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.13), residues: 3751 helix: 1.50 (0.21), residues: 666 sheet: -0.31 (0.16), residues: 1063 loop : -1.44 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 67 TYR 0.025 0.002 TYR C1067 PHE 0.024 0.002 PHE E 68 TRP 0.018 0.002 TRP D 35 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00518 (30889) covalent geometry : angle 0.62231 (42040) SS BOND : bond 0.00469 ( 43) SS BOND : angle 1.44862 ( 86) hydrogen bonds : bond 0.05505 ( 1091) hydrogen bonds : angle 5.74399 ( 3138) link_BETA1-4 : bond 0.00270 ( 15) link_BETA1-4 : angle 1.25127 ( 45) link_NAG-ASN : bond 0.00368 ( 39) link_NAG-ASN : angle 2.59488 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 ARG cc_start: 0.6837 (mmm-85) cc_final: 0.6455 (mmm-85) REVERT: A 699 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8210 (pp) REVERT: B 229 LEU cc_start: 0.8438 (mm) cc_final: 0.8216 (mp) REVERT: B 428 ASP cc_start: 0.8359 (t0) cc_final: 0.8144 (t0) REVERT: C 153 MET cc_start: 0.6437 (ppp) cc_final: 0.5804 (ppp) REVERT: C 574 ASP cc_start: 0.7809 (m-30) cc_final: 0.7417 (t0) REVERT: D 37 GLN cc_start: 0.7851 (tm130) cc_final: 0.7595 (tm-30) REVERT: E 46 GLU cc_start: 0.7343 (mp0) cc_final: 0.6931 (mp0) REVERT: E 87 ARG cc_start: 0.6817 (mtm-85) cc_final: 0.6347 (mtm-85) REVERT: G 39 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7560 (tp40) REVERT: G 112 TYR cc_start: 0.8029 (t80) cc_final: 0.7724 (t80) REVERT: I 28 THR cc_start: 0.9138 (t) cc_final: 0.8706 (p) outliers start: 45 outliers final: 33 residues processed: 289 average time/residue: 0.1868 time to fit residues: 88.8927 Evaluate side-chains 252 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 113 TRP Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 98 optimal weight: 2.9990 chunk 285 optimal weight: 0.0980 chunk 8 optimal weight: 0.0010 chunk 176 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 335 optimal weight: 5.9990 chunk 355 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN H 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.109982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.082043 restraints weight = 74491.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081558 restraints weight = 52762.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.081901 restraints weight = 65774.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082699 restraints weight = 44334.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083287 restraints weight = 38085.546| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30986 Z= 0.115 Angle : 0.567 11.768 42288 Z= 0.288 Chirality : 0.044 0.425 4906 Planarity : 0.004 0.075 5377 Dihedral : 5.630 59.840 5220 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.48 % Allowed : 12.38 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3751 helix: 1.75 (0.21), residues: 666 sheet: -0.15 (0.16), residues: 1017 loop : -1.32 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 24 TYR 0.021 0.001 TYR B1067 PHE 0.018 0.001 PHE A 238 TRP 0.014 0.001 TRP D 35 HIS 0.002 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00261 (30889) covalent geometry : angle 0.55103 (42040) SS BOND : bond 0.00337 ( 43) SS BOND : angle 1.17561 ( 86) hydrogen bonds : bond 0.04444 ( 1091) hydrogen bonds : angle 5.37503 ( 3138) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 1.26491 ( 45) link_NAG-ASN : bond 0.00300 ( 39) link_NAG-ASN : angle 2.35281 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8169 (pp) REVERT: B 229 LEU cc_start: 0.8236 (mm) cc_final: 0.8027 (mp) REVERT: C 153 MET cc_start: 0.6411 (ppp) cc_final: 0.5906 (ppp) REVERT: C 574 ASP cc_start: 0.7744 (m-30) cc_final: 0.7466 (t0) REVERT: E 12 VAL cc_start: 0.8775 (m) cc_final: 0.8554 (p) REVERT: E 87 ARG cc_start: 0.6978 (mtm-85) cc_final: 0.6689 (mtm-85) REVERT: F 4 MET cc_start: 0.6707 (mmm) cc_final: 0.6160 (mmm) REVERT: F 23 CYS cc_start: 0.3539 (t) cc_final: 0.3107 (t) REVERT: F 92 TYR cc_start: 0.6403 (t80) cc_final: 0.6193 (t80) outliers start: 48 outliers final: 30 residues processed: 290 average time/residue: 0.1788 time to fit residues: 87.1613 Evaluate side-chains 252 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 321 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 310 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 GLN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.108684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.074507 restraints weight = 74789.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077533 restraints weight = 46031.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079531 restraints weight = 30262.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079595 restraints weight = 25623.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079878 restraints weight = 24094.991| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30986 Z= 0.162 Angle : 0.593 11.779 42288 Z= 0.301 Chirality : 0.045 0.420 4906 Planarity : 0.004 0.084 5377 Dihedral : 5.321 52.009 5220 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.82 % Allowed : 13.33 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3751 helix: 1.80 (0.21), residues: 666 sheet: -0.25 (0.16), residues: 1063 loop : -1.31 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 18 TYR 0.021 0.001 TYR C1067 PHE 0.019 0.001 PHE A 238 TRP 0.020 0.001 TRP D 35 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00383 (30889) covalent geometry : angle 0.57568 (42040) SS BOND : bond 0.00383 ( 43) SS BOND : angle 1.32486 ( 86) hydrogen bonds : bond 0.04719 ( 1091) hydrogen bonds : angle 5.27253 ( 3138) link_BETA1-4 : bond 0.00318 ( 15) link_BETA1-4 : angle 1.26987 ( 45) link_NAG-ASN : bond 0.00299 ( 39) link_NAG-ASN : angle 2.44921 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 645 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8505 (p) REVERT: A 699 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8162 (pp) REVERT: C 153 MET cc_start: 0.6536 (ppp) cc_final: 0.6183 (ppp) REVERT: C 574 ASP cc_start: 0.7827 (m-30) cc_final: 0.7359 (t0) REVERT: D 37 GLN cc_start: 0.7882 (tm130) cc_final: 0.7277 (tt0) REVERT: E 12 VAL cc_start: 0.8636 (m) cc_final: 0.8411 (p) REVERT: F 4 MET cc_start: 0.6752 (mmm) cc_final: 0.6046 (mmm) REVERT: F 23 CYS cc_start: 0.3894 (t) cc_final: 0.3290 (t) REVERT: G 83 MET cc_start: 0.1729 (tpp) cc_final: 0.1387 (tpp) REVERT: H 48 ILE cc_start: 0.9187 (mm) cc_final: 0.8977 (mm) outliers start: 59 outliers final: 40 residues processed: 289 average time/residue: 0.1756 time to fit residues: 86.2049 Evaluate side-chains 261 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 323 optimal weight: 5.9990 chunk 237 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 302 optimal weight: 0.8980 chunk 333 optimal weight: 30.0000 chunk 258 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.109050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.075234 restraints weight = 74831.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077830 restraints weight = 45232.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079553 restraints weight = 33091.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.080643 restraints weight = 26992.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.081405 restraints weight = 23602.506| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30986 Z= 0.137 Angle : 0.578 11.656 42288 Z= 0.294 Chirality : 0.044 0.420 4906 Planarity : 0.004 0.054 5377 Dihedral : 5.010 55.537 5220 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.04 % Allowed : 14.04 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3751 helix: 1.81 (0.21), residues: 673 sheet: -0.17 (0.16), residues: 1065 loop : -1.29 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 67 TYR 0.020 0.001 TYR B1067 PHE 0.023 0.001 PHE E 29 TRP 0.014 0.001 TRP D 35 HIS 0.004 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00321 (30889) covalent geometry : angle 0.56244 (42040) SS BOND : bond 0.00382 ( 43) SS BOND : angle 1.21031 ( 86) hydrogen bonds : bond 0.04436 ( 1091) hydrogen bonds : angle 5.15621 ( 3138) link_BETA1-4 : bond 0.00331 ( 15) link_BETA1-4 : angle 1.27476 ( 45) link_NAG-ASN : bond 0.00268 ( 39) link_NAG-ASN : angle 2.34256 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 244 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 645 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8487 (p) REVERT: A 699 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8105 (pp) REVERT: B 452 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7707 (mmm-85) REVERT: C 153 MET cc_start: 0.6488 (ppp) cc_final: 0.6227 (ppp) REVERT: C 574 ASP cc_start: 0.7771 (m-30) cc_final: 0.7353 (t0) REVERT: C 759 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7323 (t80) REVERT: D 79 GLN cc_start: 0.6507 (mm110) cc_final: 0.5825 (mt0) REVERT: E 12 VAL cc_start: 0.8813 (m) cc_final: 0.8273 (p) REVERT: F 4 MET cc_start: 0.6554 (mmm) cc_final: 0.5529 (mmp) REVERT: F 11 LEU cc_start: 0.6986 (tp) cc_final: 0.6774 (tp) REVERT: H 79 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7541 (mm-40) outliers start: 66 outliers final: 40 residues processed: 295 average time/residue: 0.1736 time to fit residues: 85.7541 Evaluate side-chains 270 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 309 optimal weight: 0.1980 chunk 5 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 317 optimal weight: 10.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.105036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.071327 restraints weight = 75367.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073794 restraints weight = 46228.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075401 restraints weight = 34018.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076415 restraints weight = 28046.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.077148 restraints weight = 24680.587| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 30986 Z= 0.303 Angle : 0.734 12.426 42288 Z= 0.374 Chirality : 0.048 0.429 4906 Planarity : 0.005 0.067 5377 Dihedral : 5.455 56.302 5220 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.07 % Allowed : 15.22 % Favored : 82.72 % 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: -1.00 (0.13), residues: 3751 helix: 1.41 (0.21), residues: 672 sheet: -0.49 (0.15), residues: 1069 loop : -1.51 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 38 TYR 0.024 0.002 TYR C1067 PHE 0.027 0.002 PHE A1121 TRP 0.022 0.002 TRP D 35 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00713 (30889) covalent geometry : angle 0.71426 (42040) SS BOND : bond 0.00560 ( 43) SS BOND : angle 2.01428 ( 86) hydrogen bonds : bond 0.06142 ( 1091) hydrogen bonds : angle 5.55033 ( 3138) link_BETA1-4 : bond 0.00328 ( 15) link_BETA1-4 : angle 1.36785 ( 45) link_NAG-ASN : bond 0.00557 ( 39) link_NAG-ASN : angle 2.75287 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 234 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 645 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8517 (p) REVERT: A 699 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8277 (pp) REVERT: C 153 MET cc_start: 0.6565 (ppp) cc_final: 0.6350 (ppp) REVERT: C 574 ASP cc_start: 0.7932 (m-30) cc_final: 0.7485 (t0) REVERT: D 37 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7408 (tt0) REVERT: F 4 MET cc_start: 0.6604 (mmm) cc_final: 0.5714 (mmm) REVERT: G 83 MET cc_start: 0.1849 (tpp) cc_final: 0.1461 (tpp) REVERT: I 34 MET cc_start: 0.8022 (mmm) cc_final: 0.7772 (mmm) outliers start: 67 outliers final: 47 residues processed: 286 average time/residue: 0.1762 time to fit residues: 84.9299 Evaluate side-chains 262 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 113 TRP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 0 optimal weight: 30.0000 chunk 319 optimal weight: 1.9990 chunk 347 optimal weight: 0.9980 chunk 231 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 299 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 318 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN H 37 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.107773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074082 restraints weight = 75191.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.076668 restraints weight = 45511.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078369 restraints weight = 33232.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079430 restraints weight = 27135.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.080193 restraints weight = 23805.407| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30986 Z= 0.128 Angle : 0.604 11.898 42288 Z= 0.305 Chirality : 0.045 0.426 4906 Planarity : 0.004 0.054 5377 Dihedral : 5.018 55.141 5220 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.79 % Allowed : 16.08 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3751 helix: 1.75 (0.21), residues: 672 sheet: -0.35 (0.16), residues: 1069 loop : -1.39 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.021 0.001 TYR B1067 PHE 0.019 0.001 PHE E 29 TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00296 (30889) covalent geometry : angle 0.58704 (42040) SS BOND : bond 0.00340 ( 43) SS BOND : angle 1.54935 ( 86) hydrogen bonds : bond 0.04644 ( 1091) hydrogen bonds : angle 5.15817 ( 3138) link_BETA1-4 : bond 0.00396 ( 15) link_BETA1-4 : angle 1.30080 ( 45) link_NAG-ASN : bond 0.00272 ( 39) link_NAG-ASN : angle 2.35739 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 645 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8474 (p) REVERT: A 699 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8185 (pp) REVERT: B 452 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7729 (mmm-85) REVERT: C 574 ASP cc_start: 0.7810 (m-30) cc_final: 0.7165 (t0) REVERT: D 37 GLN cc_start: 0.7951 (tm130) cc_final: 0.7304 (tt0) REVERT: E 87 ARG cc_start: 0.6078 (mtm-85) cc_final: 0.5857 (ptt-90) REVERT: F 4 MET cc_start: 0.6621 (mmm) cc_final: 0.5544 (mmp) REVERT: F 24 ARG cc_start: 0.4374 (OUTLIER) cc_final: 0.4123 (mmp-170) REVERT: F 61 ARG cc_start: 0.4665 (mmp80) cc_final: 0.4332 (mmp80) REVERT: G 80 TYR cc_start: 0.7605 (m-80) cc_final: 0.6809 (m-80) REVERT: G 87 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.7776 (ptt-90) REVERT: I 34 MET cc_start: 0.7837 (mmm) cc_final: 0.7561 (mmm) REVERT: I 83 MET cc_start: 0.7299 (mpp) cc_final: 0.6724 (mpp) outliers start: 58 outliers final: 43 residues processed: 280 average time/residue: 0.1774 time to fit residues: 82.7401 Evaluate side-chains 268 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 371 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 240 optimal weight: 6.9990 chunk 354 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 344 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.105762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.071325 restraints weight = 75283.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.074141 restraints weight = 49442.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.076131 restraints weight = 33483.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076182 restraints weight = 28045.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076325 restraints weight = 27334.691| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 30986 Z= 0.258 Angle : 0.692 13.586 42288 Z= 0.352 Chirality : 0.047 0.422 4906 Planarity : 0.004 0.065 5377 Dihedral : 5.219 51.510 5220 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.79 % Allowed : 16.33 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 3751 helix: 1.56 (0.21), residues: 673 sheet: -0.52 (0.15), residues: 1073 loop : -1.51 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 16 TYR 0.023 0.002 TYR C1067 PHE 0.023 0.002 PHE A1121 TRP 0.034 0.002 TRP B 436 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00615 (30889) covalent geometry : angle 0.67391 (42040) SS BOND : bond 0.00498 ( 43) SS BOND : angle 1.79711 ( 86) hydrogen bonds : bond 0.05593 ( 1091) hydrogen bonds : angle 5.33678 ( 3138) link_BETA1-4 : bond 0.00327 ( 15) link_BETA1-4 : angle 1.30524 ( 45) link_NAG-ASN : bond 0.00437 ( 39) link_NAG-ASN : angle 2.60920 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 224 time to evaluate : 1.307 Fit side-chains REVERT: A 645 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 699 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8355 (pp) REVERT: C 574 ASP cc_start: 0.7992 (m-30) cc_final: 0.7348 (t0) REVERT: F 4 MET cc_start: 0.6606 (mmm) cc_final: 0.5877 (mmm) REVERT: F 24 ARG cc_start: 0.4725 (OUTLIER) cc_final: 0.4399 (mmp-170) REVERT: F 61 ARG cc_start: 0.4731 (mmp80) cc_final: 0.4357 (mmp80) REVERT: I 34 MET cc_start: 0.8052 (mmm) cc_final: 0.7793 (mmm) outliers start: 58 outliers final: 47 residues processed: 271 average time/residue: 0.1829 time to fit residues: 82.6678 Evaluate side-chains 263 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 113 TRP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 370 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 196 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.107807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.074279 restraints weight = 74682.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.076833 restraints weight = 45085.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.078536 restraints weight = 32988.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.079642 restraints weight = 26957.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080329 restraints weight = 23586.516| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30986 Z= 0.126 Angle : 0.613 11.642 42288 Z= 0.310 Chirality : 0.045 0.429 4906 Planarity : 0.004 0.064 5377 Dihedral : 4.860 42.473 5220 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.36 % Allowed : 16.91 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3751 helix: 1.78 (0.21), residues: 674 sheet: -0.28 (0.16), residues: 1066 loop : -1.42 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 452 TYR 0.023 0.001 TYR H 92 PHE 0.017 0.001 PHE A 238 TRP 0.038 0.001 TRP B 436 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00289 (30889) covalent geometry : angle 0.59840 (42040) SS BOND : bond 0.00317 ( 43) SS BOND : angle 1.35150 ( 86) hydrogen bonds : bond 0.04463 ( 1091) hydrogen bonds : angle 5.07828 ( 3138) link_BETA1-4 : bond 0.00360 ( 15) link_BETA1-4 : angle 1.27800 ( 45) link_NAG-ASN : bond 0.00283 ( 39) link_NAG-ASN : angle 2.31789 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7502 Ramachandran restraints generated. 3751 Oldfield, 0 Emsley, 3751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 645 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 699 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8270 (pp) REVERT: B 452 ARG cc_start: 0.8218 (mmm-85) cc_final: 0.7717 (mmm-85) REVERT: C 418 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7668 (tp) REVERT: C 574 ASP cc_start: 0.7869 (m-30) cc_final: 0.7141 (t0) REVERT: D 37 GLN cc_start: 0.8036 (tm130) cc_final: 0.7373 (tt0) REVERT: F 4 MET cc_start: 0.6638 (mmm) cc_final: 0.5801 (mmm) REVERT: F 61 ARG cc_start: 0.4825 (mmp80) cc_final: 0.4467 (mmp80) REVERT: I 34 MET cc_start: 0.7932 (mmm) cc_final: 0.7659 (mmm) outliers start: 44 outliers final: 39 residues processed: 264 average time/residue: 0.1843 time to fit residues: 81.1513 Evaluate side-chains 257 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 PHE Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 307 optimal weight: 0.3980 chunk 294 optimal weight: 0.7980 chunk 349 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 329 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 327 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.108394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074907 restraints weight = 75471.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077509 restraints weight = 45274.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079238 restraints weight = 32946.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080273 restraints weight = 26819.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081066 restraints weight = 23540.011| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30986 Z= 0.118 Angle : 0.597 11.415 42288 Z= 0.301 Chirality : 0.044 0.424 4906 Planarity : 0.004 0.063 5377 Dihedral : 4.576 38.116 5220 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.39 % Allowed : 16.73 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3751 helix: 1.93 (0.21), residues: 674 sheet: -0.18 (0.16), residues: 1050 loop : -1.33 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 16 TYR 0.020 0.001 TYR G 95 PHE 0.024 0.001 PHE C 429 TRP 0.034 0.001 TRP B 436 HIS 0.003 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00276 (30889) covalent geometry : angle 0.58217 (42040) SS BOND : bond 0.00294 ( 43) SS BOND : angle 1.24158 ( 86) hydrogen bonds : bond 0.04127 ( 1091) hydrogen bonds : angle 4.87457 ( 3138) link_BETA1-4 : bond 0.00396 ( 15) link_BETA1-4 : angle 1.28690 ( 45) link_NAG-ASN : bond 0.00261 ( 39) link_NAG-ASN : angle 2.29248 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6012.47 seconds wall clock time: 104 minutes 32.31 seconds (6272.31 seconds total)