Starting phenix.real_space_refine on Fri Mar 6 22:41:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mjk_23876/03_2026/7mjk_23876.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjk_23876/03_2026/7mjk_23876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mjk_23876/03_2026/7mjk_23876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjk_23876/03_2026/7mjk_23876.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mjk_23876/03_2026/7mjk_23876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjk_23876/03_2026/7mjk_23876.map" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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 144 5.16 5 C 22143 2.51 5 N 5721 2.21 5 O 6870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 34878 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Chain: "E" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "G" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "I" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "F" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Chain: "H" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Chain: "B" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "Y" 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: "Z" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 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: 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 Time building chain proxies: 8.10, per 1000 atoms: 0.23 Number of scatterers: 34878 At special positions: 0 Unit cell: (149, 148, 245, 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 144 16.00 O 6870 8.00 N 5721 7.00 C 22143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 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 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG J 1 " - " ASN A 17 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.4 seconds 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8178 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 84 sheets defined 19.8% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.820A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.635A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.082A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.136A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.668A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.907A 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: 3.533A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.093A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.533A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 86 through 90 removed outlier: 4.109A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.860A pdb=" N VAL E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.861A pdb=" N VAL G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.864A pdb=" N VAL I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.532A pdb=" N SER F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN F 32 " --> pdb=" O VAL F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 86 through 90 removed outlier: 4.108A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.542A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.102A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 193 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.816A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.635A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.083A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.135A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.666A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.910A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.530A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.091A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.839A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.643A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.085A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.135A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.673A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.907A 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: 3.533A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.091A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.165A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.289A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.991A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.501A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 163 removed outlier: 5.380A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.639A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.296A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.151A 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 654 through 655 removed outlier: 6.009A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.548A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.564A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.564A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.386A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.875A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.130A pdb=" N TYR D 33 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.861A pdb=" N TYR D 99 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE D 104 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 124 through 128 removed outlier: 6.098A pdb=" N TYR D 180 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 124 through 128 removed outlier: 6.098A pdb=" N TYR D 180 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 198 through 204 removed outlier: 4.072A pdb=" N TYR D 198 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 4 through 7 removed outlier: 5.951A pdb=" N THR E 69 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 10.593A pdb=" N GLN E 27 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N SER E 67 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 11.615A pdb=" N VAL E 29 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N SER E 65 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.991A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.991A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.877A pdb=" N SER E 131 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU E 181 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL E 133 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU E 179 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER E 177 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN E 137 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU E 175 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 145 through 150 Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 7 removed outlier: 5.951A pdb=" N THR G 69 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N GLN G 27 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N SER G 67 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N VAL G 29 " --> pdb=" O SER G 65 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N SER G 65 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 13 removed outlier: 5.990A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 13 removed outlier: 5.990A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 114 through 118 removed outlier: 5.838A pdb=" N SER G 131 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU G 181 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL G 133 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU G 179 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU G 135 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER G 177 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN G 137 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU G 175 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 145 through 150 Processing sheet with id=AD9, first strand: chain 'I' and resid 4 through 7 removed outlier: 5.985A pdb=" N THR I 69 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLN I 27 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N SER I 67 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N VAL I 29 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N SER I 65 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.983A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.983A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 114 through 118 removed outlier: 5.868A pdb=" N SER I 131 " --> pdb=" O LEU I 181 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU I 181 " --> pdb=" O SER I 131 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL I 133 " --> pdb=" O LEU I 179 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU I 179 " --> pdb=" O VAL I 133 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU I 135 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER I 177 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASN I 137 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU I 175 " --> pdb=" O ASN I 137 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 145 through 150 Processing sheet with id=AE5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.130A pdb=" N TYR F 33 " --> pdb=" O GLY F 98 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.860A pdb=" N TYR F 99 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE F 104 " --> pdb=" O TYR F 99 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 124 through 128 removed outlier: 6.093A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 124 through 128 removed outlier: 6.093A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 198 through 204 removed outlier: 4.054A pdb=" N TYR F 198 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.138A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.517A pdb=" N TYR H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR H 99 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE H 104 " --> pdb=" O TYR H 99 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.082A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.082A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 198 through 204 removed outlier: 4.055A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AF9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.172A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.987A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.728A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 154 through 163 removed outlier: 9.411A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 11.462A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.640A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 325 through 326 removed outlier: 5.299A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AG7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.154A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AG9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AH1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.013A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.548A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.393A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AH7, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AH8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.154A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.988A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.727A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.414A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.463A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.640A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AI5, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.148A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AI7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AI8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.018A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.553A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.553A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.389A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'C' and resid 1120 through 1122 1533 hydrogen bonds defined for protein. 4029 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: 9.99 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10141 1.34 - 1.46: 7771 1.46 - 1.58: 17584 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 35676 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.67e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.60e+00 ... (remaining 35671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 46960 2.04 - 4.07: 1411 4.07 - 6.11: 141 6.11 - 8.14: 46 8.14 - 10.18: 9 Bond angle restraints: 48567 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.04 -5.34 1.22e+00 6.72e-01 1.92e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.03 -5.33 1.22e+00 6.72e-01 1.91e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.01 -5.31 1.22e+00 6.72e-01 1.90e+01 angle pdb=" N GLN B1010 " pdb=" CA GLN B1010 " pdb=" CB GLN B1010 " ideal model delta sigma weight residual 110.39 116.39 -6.00 1.66e+00 3.63e-01 1.31e+01 angle pdb=" CA PRO B 986 " pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 117.93 122.24 -4.31 1.20e+00 6.94e-01 1.29e+01 ... (remaining 48562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 20384 17.87 - 35.75: 1318 35.75 - 53.62: 234 53.62 - 71.50: 64 71.50 - 89.37: 44 Dihedral angle restraints: 22044 sinusoidal: 9297 harmonic: 12747 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.61 -59.61 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.44 -59.44 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.36 -59.36 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 22041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5109 0.094 - 0.189: 525 0.189 - 0.283: 25 0.283 - 0.377: 5 0.377 - 0.472: 3 Chirality restraints: 5667 Sorted by residual: chirality pdb=" CB VAL D 63 " pdb=" CA VAL D 63 " pdb=" CG1 VAL D 63 " pdb=" CG2 VAL D 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CB VAL F 63 " pdb=" CA VAL F 63 " pdb=" CG1 VAL F 63 " pdb=" CG2 VAL F 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CB VAL H 63 " pdb=" CA VAL H 63 " pdb=" CG1 VAL H 63 " pdb=" CG2 VAL H 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.46 2.00e-01 2.50e+01 5.40e+00 ... (remaining 5664 not shown) Planarity restraints: 6231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 203 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO E 204 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO E 204 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO E 204 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 203 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO I 204 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO I 204 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO I 204 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 203 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO G 204 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO G 204 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 204 " -0.059 5.00e-02 4.00e+02 ... (remaining 6228 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10042 2.83 - 3.34: 28741 3.34 - 3.86: 59634 3.86 - 4.38: 68274 4.38 - 4.90: 118506 Nonbonded interactions: 285197 Sorted by model distance: nonbonded pdb=" OG SER F 56 " pdb=" OD2 ASP B 420 " model vdw 2.307 3.040 nonbonded pdb=" OD2 ASP A 420 " pdb=" OG SER D 56 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.308 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.314 3.040 ... (remaining 285192 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.660 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 0.077 35790 Z= 0.209 Angle : 0.811 15.004 48855 Z= 0.426 Chirality : 0.055 0.472 5667 Planarity : 0.008 0.111 6189 Dihedral : 12.845 89.373 13704 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % 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: -0.85 (0.12), residues: 4323 helix: -0.04 (0.18), residues: 684 sheet: -0.04 (0.14), residues: 1329 loop : -1.01 (0.11), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 211 TYR 0.024 0.002 TYR A 495 PHE 0.035 0.002 PHE C 275 TRP 0.020 0.002 TRP B 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00441 (35676) covalent geometry : angle 0.79201 (48567) SS BOND : bond 0.00246 ( 54) SS BOND : angle 1.22708 ( 108) hydrogen bonds : bond 0.13387 ( 1413) hydrogen bonds : angle 7.45334 ( 4029) link_BETA1-4 : bond 0.00649 ( 18) link_BETA1-4 : angle 1.46414 ( 54) link_NAG-ASN : bond 0.00720 ( 42) link_NAG-ASN : angle 3.35895 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 GLN cc_start: 0.8429 (tp40) cc_final: 0.7924 (tm-30) REVERT: D 82 MET cc_start: 0.0714 (mtp) cc_final: 0.0502 (mtp) REVERT: E 4 MET cc_start: 0.3508 (mmm) cc_final: 0.2606 (ttp) REVERT: E 17 GLU cc_start: 0.6274 (pt0) cc_final: 0.5805 (pm20) REVERT: E 123 GLU cc_start: 0.4775 (pp20) cc_final: 0.4095 (pm20) REVERT: E 187 GLU cc_start: 0.6510 (mm-30) cc_final: 0.4595 (pp20) REVERT: G 17 GLU cc_start: 0.6118 (pt0) cc_final: 0.5826 (pm20) REVERT: G 18 LYS cc_start: 0.6314 (tttt) cc_final: 0.5999 (tptp) REVERT: G 123 GLU cc_start: 0.5005 (pp20) cc_final: 0.4418 (pm20) REVERT: G 140 TYR cc_start: 0.5321 (t80) cc_final: 0.3884 (t80) REVERT: G 187 GLU cc_start: 0.6590 (mm-30) cc_final: 0.4495 (pp20) REVERT: I 4 MET cc_start: 0.4370 (mmm) cc_final: 0.3682 (ttp) REVERT: I 17 GLU cc_start: 0.6296 (pt0) cc_final: 0.5875 (pm20) REVERT: I 187 GLU cc_start: 0.6396 (mm-30) cc_final: 0.5673 (mp0) REVERT: F 19 ARG cc_start: 0.8141 (ttt-90) cc_final: 0.7902 (tpt170) REVERT: F 81 GLN cc_start: 0.8328 (tp40) cc_final: 0.7805 (tm-30) REVERT: F 89 ASP cc_start: 0.3711 (m-30) cc_final: 0.3252 (m-30) REVERT: B 390 LEU cc_start: 0.8793 (mt) cc_final: 0.8414 (tm) outliers start: 0 outliers final: 3 residues processed: 286 average time/residue: 0.7609 time to fit residues: 254.2386 Evaluate side-chains 111 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain C residue 440 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 0.9980 chunk 424 optimal weight: 0.7980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 926 GLN E 6 GLN G 6 GLN I 6 GLN I 38 GLN I 42 GLN H 39 GLN H 72 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 926 GLN C 207 HIS C 926 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.119979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.080434 restraints weight = 134096.605| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 5.42 r_work: 0.2954 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35790 Z= 0.237 Angle : 0.642 10.445 48855 Z= 0.327 Chirality : 0.045 0.199 5667 Planarity : 0.005 0.077 6189 Dihedral : 5.815 52.957 5979 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.84 % Allowed : 5.92 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % 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: -0.10 (0.12), residues: 4323 helix: 1.42 (0.20), residues: 678 sheet: 0.20 (0.14), residues: 1338 loop : -0.66 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 346 TYR 0.018 0.002 TYR C 265 PHE 0.023 0.002 PHE A 275 TRP 0.017 0.001 TRP A 886 HIS 0.006 0.001 HIS H 72 Details of bonding type rmsd covalent geometry : bond 0.00532 (35676) covalent geometry : angle 0.62603 (48567) SS BOND : bond 0.00186 ( 54) SS BOND : angle 0.78897 ( 108) hydrogen bonds : bond 0.04231 ( 1413) hydrogen bonds : angle 5.91165 ( 4029) link_BETA1-4 : bond 0.00190 ( 18) link_BETA1-4 : angle 1.37353 ( 54) link_NAG-ASN : bond 0.00606 ( 42) link_NAG-ASN : angle 2.70921 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8399 (pmm150) cc_final: 0.8161 (pmm150) REVERT: A 449 TYR cc_start: 0.8893 (m-80) cc_final: 0.8633 (m-80) REVERT: D 82 MET cc_start: 0.1127 (mtp) cc_final: 0.0899 (mtt) REVERT: D 101 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6875 (m-30) REVERT: G 4 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.5959 (ptm) REVERT: I 4 MET cc_start: 0.6750 (mmm) cc_final: 0.6113 (ttp) REVERT: F 19 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.7900 (tpm170) REVERT: F 89 ASP cc_start: 0.4371 (m-30) cc_final: 0.4048 (m-30) REVERT: F 101 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6788 (m-30) REVERT: H 34 MET cc_start: 0.5172 (OUTLIER) cc_final: 0.4861 (tpp) REVERT: B 214 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8287 (ptm-80) REVERT: B 390 LEU cc_start: 0.9107 (mt) cc_final: 0.8766 (tm) outliers start: 32 outliers final: 9 residues processed: 161 average time/residue: 0.6884 time to fit residues: 132.8159 Evaluate side-chains 118 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 85 optimal weight: 3.9990 chunk 394 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 122 optimal weight: 30.0000 chunk 316 optimal weight: 2.9990 chunk 412 optimal weight: 1.9990 chunk 393 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1010 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN G 27 GLN I 27 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.107883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.064905 restraints weight = 113254.919| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.32 r_work: 0.2927 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35790 Z= 0.244 Angle : 0.610 9.748 48855 Z= 0.311 Chirality : 0.045 0.196 5667 Planarity : 0.005 0.078 6189 Dihedral : 5.289 53.295 5973 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.49 % Allowed : 7.57 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % 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: 0.12 (0.12), residues: 4323 helix: 1.74 (0.20), residues: 684 sheet: 0.25 (0.14), residues: 1320 loop : -0.50 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 19 TYR 0.022 0.002 TYR A 904 PHE 0.020 0.002 PHE B 275 TRP 0.016 0.001 TRP B 886 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00548 (35676) covalent geometry : angle 0.59443 (48567) SS BOND : bond 0.00125 ( 54) SS BOND : angle 0.70711 ( 108) hydrogen bonds : bond 0.04162 ( 1413) hydrogen bonds : angle 5.70488 ( 4029) link_BETA1-4 : bond 0.00363 ( 18) link_BETA1-4 : angle 1.18577 ( 54) link_NAG-ASN : bond 0.00591 ( 42) link_NAG-ASN : angle 2.67308 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 115 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8807 (m-80) cc_final: 0.8474 (m-80) REVERT: A 979 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8171 (OUTLIER) REVERT: D 82 MET cc_start: 0.1365 (mtp) cc_final: 0.1049 (mtt) REVERT: D 90 THR cc_start: 0.5648 (OUTLIER) cc_final: 0.5411 (m) REVERT: D 101 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6970 (m-30) REVERT: E 4 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.5410 (ptm) REVERT: E 24 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8214 (tpp80) REVERT: G 4 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6010 (ptm) REVERT: I 4 MET cc_start: 0.7057 (mmm) cc_final: 0.6751 (ttm) REVERT: F 90 THR cc_start: 0.5709 (OUTLIER) cc_final: 0.5457 (m) REVERT: F 101 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: H 90 THR cc_start: 0.4894 (OUTLIER) cc_final: 0.4610 (m) REVERT: B 214 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8340 (ptm-80) REVERT: C 697 MET cc_start: 0.9183 (ptt) cc_final: 0.8974 (ptt) REVERT: C 731 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8750 (ptm) outliers start: 57 outliers final: 9 residues processed: 157 average time/residue: 0.5989 time to fit residues: 115.3032 Evaluate side-chains 110 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 731 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 27 optimal weight: 4.9990 chunk 295 optimal weight: 0.8980 chunk 437 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 431 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 chunk 132 optimal weight: 40.0000 chunk 189 optimal weight: 20.0000 chunk 367 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 957 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 203 ASN B 907 ASN B 957 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 907 ASN C 957 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.107640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060470 restraints weight = 109719.462| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.14 r_work: 0.2914 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 35790 Z= 0.340 Angle : 0.665 10.076 48855 Z= 0.337 Chirality : 0.046 0.190 5667 Planarity : 0.005 0.081 6189 Dihedral : 5.385 53.099 5973 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.91 % Allowed : 8.43 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.12), residues: 4323 helix: 1.43 (0.20), residues: 717 sheet: 0.05 (0.14), residues: 1320 loop : -0.56 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 71 TYR 0.025 0.002 TYR A 904 PHE 0.030 0.002 PHE D 67 TRP 0.014 0.002 TRP B 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00765 (35676) covalent geometry : angle 0.64973 (48567) SS BOND : bond 0.00217 ( 54) SS BOND : angle 0.77246 ( 108) hydrogen bonds : bond 0.04439 ( 1413) hydrogen bonds : angle 5.76754 ( 4029) link_BETA1-4 : bond 0.00173 ( 18) link_BETA1-4 : angle 1.34527 ( 54) link_NAG-ASN : bond 0.00743 ( 42) link_NAG-ASN : angle 2.77744 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 94 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8951 (m-80) cc_final: 0.8644 (m-80) REVERT: A 697 MET cc_start: 0.9230 (ptt) cc_final: 0.9012 (ptt) REVERT: A 1017 GLU cc_start: 0.9089 (tt0) cc_final: 0.8824 (tm-30) REVERT: D 101 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7053 (m-30) REVERT: E 4 MET cc_start: 0.6439 (mtm) cc_final: 0.6069 (mtt) REVERT: G 4 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6220 (ptm) REVERT: F 101 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: C 126 VAL cc_start: 0.7548 (OUTLIER) cc_final: 0.7338 (t) REVERT: C 298 GLU cc_start: 0.9179 (tt0) cc_final: 0.8575 (tp30) REVERT: C 697 MET cc_start: 0.9211 (ptt) cc_final: 0.9008 (ptt) outliers start: 73 outliers final: 22 residues processed: 149 average time/residue: 0.5894 time to fit residues: 107.8549 Evaluate side-chains 102 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 56 optimal weight: 0.6980 chunk 410 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 310 optimal weight: 0.6980 chunk 405 optimal weight: 0.9990 chunk 395 optimal weight: 0.7980 chunk 192 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 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 = 0.4271 r_free = 0.4271 target = 0.113388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.071896 restraints weight = 110184.140| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 4.25 r_work: 0.2959 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35790 Z= 0.115 Angle : 0.542 9.924 48855 Z= 0.275 Chirality : 0.043 0.207 5667 Planarity : 0.004 0.081 6189 Dihedral : 4.963 53.225 5973 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.26 % Allowed : 9.66 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % 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: 0.21 (0.13), residues: 4323 helix: 2.01 (0.20), residues: 699 sheet: 0.16 (0.14), residues: 1266 loop : -0.40 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 19 TYR 0.019 0.001 TYR C1067 PHE 0.033 0.001 PHE D 67 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 72 Details of bonding type rmsd covalent geometry : bond 0.00247 (35676) covalent geometry : angle 0.52702 (48567) SS BOND : bond 0.00087 ( 54) SS BOND : angle 0.52581 ( 108) hydrogen bonds : bond 0.03576 ( 1413) hydrogen bonds : angle 5.45336 ( 4029) link_BETA1-4 : bond 0.00448 ( 18) link_BETA1-4 : angle 0.98607 ( 54) link_NAG-ASN : bond 0.00517 ( 42) link_NAG-ASN : angle 2.52319 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8829 (m-80) cc_final: 0.8513 (m-80) REVERT: A 1017 GLU cc_start: 0.9096 (tt0) cc_final: 0.8815 (tm-30) REVERT: D 34 MET cc_start: 0.5363 (OUTLIER) cc_final: 0.5099 (mmt) REVERT: D 90 THR cc_start: 0.5865 (OUTLIER) cc_final: 0.5606 (m) REVERT: D 101 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: G 4 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.5618 (ptm) REVERT: I 4 MET cc_start: 0.6934 (tpp) cc_final: 0.6181 (ttm) REVERT: F 34 MET cc_start: 0.5447 (OUTLIER) cc_final: 0.4269 (mtp) REVERT: F 90 THR cc_start: 0.5903 (OUTLIER) cc_final: 0.5634 (m) REVERT: F 101 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: C 298 GLU cc_start: 0.9203 (tt0) cc_final: 0.8553 (tp30) REVERT: C 697 MET cc_start: 0.9246 (ptt) cc_final: 0.9030 (ptt) outliers start: 48 outliers final: 13 residues processed: 135 average time/residue: 0.6112 time to fit residues: 101.3839 Evaluate side-chains 104 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 250 optimal weight: 6.9990 chunk 358 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 182 optimal weight: 30.0000 chunk 430 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.113997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067393 restraints weight = 108916.368| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.78 r_work: 0.2935 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 35790 Z= 0.254 Angle : 0.597 9.596 48855 Z= 0.301 Chirality : 0.045 0.192 5667 Planarity : 0.004 0.084 6189 Dihedral : 5.044 53.483 5973 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.26 % Allowed : 10.55 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % 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: 0.20 (0.13), residues: 4323 helix: 1.96 (0.20), residues: 699 sheet: 0.10 (0.14), residues: 1302 loop : -0.36 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 86 TYR 0.028 0.001 TYR A 904 PHE 0.034 0.002 PHE D 67 TRP 0.015 0.001 TRP I 50 HIS 0.004 0.001 HIS H 72 Details of bonding type rmsd covalent geometry : bond 0.00573 (35676) covalent geometry : angle 0.58054 (48567) SS BOND : bond 0.00136 ( 54) SS BOND : angle 0.62346 ( 108) hydrogen bonds : bond 0.04065 ( 1413) hydrogen bonds : angle 5.52585 ( 4029) link_BETA1-4 : bond 0.00145 ( 18) link_BETA1-4 : angle 1.25594 ( 54) link_NAG-ASN : bond 0.00660 ( 42) link_NAG-ASN : angle 2.66269 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8860 (m-80) cc_final: 0.8559 (m-80) REVERT: A 1017 GLU cc_start: 0.9080 (tt0) cc_final: 0.8802 (tm-30) REVERT: D 34 MET cc_start: 0.5213 (OUTLIER) cc_final: 0.4525 (mtp) REVERT: D 90 THR cc_start: 0.6165 (OUTLIER) cc_final: 0.5924 (m) REVERT: D 101 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: E 4 MET cc_start: 0.6106 (mtm) cc_final: 0.5247 (ptp) REVERT: G 4 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.5622 (ptm) REVERT: I 4 MET cc_start: 0.7021 (tpp) cc_final: 0.6083 (ttp) REVERT: F 34 MET cc_start: 0.5300 (OUTLIER) cc_final: 0.4593 (mtp) REVERT: F 90 THR cc_start: 0.6116 (OUTLIER) cc_final: 0.5874 (m) REVERT: F 101 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7096 (m-30) REVERT: H 34 MET cc_start: 0.4732 (OUTLIER) cc_final: 0.4429 (mmp) REVERT: B 697 MET cc_start: 0.9192 (ptt) cc_final: 0.8969 (ptt) REVERT: C 298 GLU cc_start: 0.9178 (tt0) cc_final: 0.8577 (tp30) REVERT: C 390 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8554 (tm) outliers start: 48 outliers final: 19 residues processed: 129 average time/residue: 0.6225 time to fit residues: 98.5363 Evaluate side-chains 107 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 234 optimal weight: 3.9990 chunk 364 optimal weight: 8.9990 chunk 394 optimal weight: 1.9990 chunk 372 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 305 optimal weight: 0.3980 chunk 249 optimal weight: 0.6980 chunk 341 optimal weight: 3.9990 chunk 416 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.114299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068399 restraints weight = 109438.416| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.70 r_work: 0.2980 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35790 Z= 0.135 Angle : 0.536 9.921 48855 Z= 0.271 Chirality : 0.043 0.205 5667 Planarity : 0.004 0.083 6189 Dihedral : 4.835 53.211 5973 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.07 % Allowed : 11.05 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.13), residues: 4323 helix: 2.15 (0.20), residues: 699 sheet: 0.18 (0.14), residues: 1260 loop : -0.32 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 983 TYR 0.021 0.001 TYR A 904 PHE 0.020 0.001 PHE F 67 TRP 0.010 0.001 TRP H 107 HIS 0.005 0.001 HIS H 72 Details of bonding type rmsd covalent geometry : bond 0.00301 (35676) covalent geometry : angle 0.52061 (48567) SS BOND : bond 0.00065 ( 54) SS BOND : angle 0.50047 ( 108) hydrogen bonds : bond 0.03557 ( 1413) hydrogen bonds : angle 5.33728 ( 4029) link_BETA1-4 : bond 0.00301 ( 18) link_BETA1-4 : angle 0.96561 ( 54) link_NAG-ASN : bond 0.00518 ( 42) link_NAG-ASN : angle 2.51161 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.9079 (tt0) cc_final: 0.8811 (tm-30) REVERT: D 34 MET cc_start: 0.5275 (OUTLIER) cc_final: 0.4639 (mtp) REVERT: D 90 THR cc_start: 0.6095 (OUTLIER) cc_final: 0.5841 (m) REVERT: D 101 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6854 (m-30) REVERT: E 4 MET cc_start: 0.5874 (mtm) cc_final: 0.4989 (ptm) REVERT: G 4 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.5070 (ptm) REVERT: I 4 MET cc_start: 0.6898 (tpp) cc_final: 0.5970 (ttp) REVERT: F 34 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.4884 (mtp) REVERT: F 90 THR cc_start: 0.6384 (OUTLIER) cc_final: 0.6134 (m) REVERT: F 101 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7031 (m-30) REVERT: H 34 MET cc_start: 0.4847 (OUTLIER) cc_final: 0.4488 (mmp) REVERT: H 67 PHE cc_start: 0.4321 (m-10) cc_final: 0.3624 (m-10) REVERT: H 82 MET cc_start: -0.0939 (mmm) cc_final: -0.2327 (mtp) REVERT: B 298 GLU cc_start: 0.9011 (tt0) cc_final: 0.8524 (tp30) REVERT: B 697 MET cc_start: 0.9177 (ptt) cc_final: 0.8973 (ptt) REVERT: C 298 GLU cc_start: 0.9087 (tt0) cc_final: 0.8510 (tp30) REVERT: C 697 MET cc_start: 0.9310 (ptt) cc_final: 0.9007 (ptt) outliers start: 41 outliers final: 18 residues processed: 125 average time/residue: 0.6506 time to fit residues: 98.8011 Evaluate side-chains 111 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 315 optimal weight: 1.9990 chunk 437 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 296 optimal weight: 0.9990 chunk 427 optimal weight: 0.0270 chunk 236 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 309 optimal weight: 0.9980 chunk 424 optimal weight: 2.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.114781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069031 restraints weight = 109068.663| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.70 r_work: 0.2992 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35790 Z= 0.117 Angle : 0.528 10.533 48855 Z= 0.266 Chirality : 0.043 0.215 5667 Planarity : 0.004 0.087 6189 Dihedral : 4.634 53.572 5973 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.02 % Allowed : 11.26 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % 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: 0.38 (0.13), residues: 4323 helix: 2.09 (0.20), residues: 717 sheet: 0.31 (0.14), residues: 1239 loop : -0.31 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 983 TYR 0.018 0.001 TYR A 904 PHE 0.021 0.001 PHE C 565 TRP 0.010 0.001 TRP D 107 HIS 0.004 0.001 HIS H 72 Details of bonding type rmsd covalent geometry : bond 0.00260 (35676) covalent geometry : angle 0.51245 (48567) SS BOND : bond 0.00086 ( 54) SS BOND : angle 0.49439 ( 108) hydrogen bonds : bond 0.03410 ( 1413) hydrogen bonds : angle 5.18601 ( 4029) link_BETA1-4 : bond 0.00287 ( 18) link_BETA1-4 : angle 1.01599 ( 54) link_NAG-ASN : bond 0.00511 ( 42) link_NAG-ASN : angle 2.47309 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 94 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8803 (m-80) cc_final: 0.8532 (m-80) REVERT: A 1017 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8799 (tm-30) REVERT: D 34 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.4549 (mtp) REVERT: D 90 THR cc_start: 0.6429 (OUTLIER) cc_final: 0.6202 (m) REVERT: D 101 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: E 4 MET cc_start: 0.5965 (mtm) cc_final: 0.5192 (ptm) REVERT: G 4 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.5452 (ptm) REVERT: I 4 MET cc_start: 0.7139 (tpp) cc_final: 0.6305 (ttp) REVERT: F 34 MET cc_start: 0.5422 (OUTLIER) cc_final: 0.4855 (mtp) REVERT: F 90 THR cc_start: 0.6563 (OUTLIER) cc_final: 0.6331 (m) REVERT: F 101 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: H 34 MET cc_start: 0.4881 (OUTLIER) cc_final: 0.4488 (mmp) REVERT: H 67 PHE cc_start: 0.4365 (m-10) cc_final: 0.3749 (m-10) REVERT: H 82 MET cc_start: -0.0767 (mmm) cc_final: -0.2085 (mtp) REVERT: B 697 MET cc_start: 0.9142 (ptt) cc_final: 0.8915 (ptt) REVERT: B 934 ILE cc_start: 0.8801 (mm) cc_final: 0.8564 (mp) outliers start: 39 outliers final: 21 residues processed: 123 average time/residue: 0.6242 time to fit residues: 94.1259 Evaluate side-chains 113 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 316 optimal weight: 1.9990 chunk 437 optimal weight: 4.9990 chunk 330 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 0.0030 chunk 264 optimal weight: 5.9990 chunk 402 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 269 optimal weight: 0.1980 chunk 68 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.114150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.068478 restraints weight = 108485.031| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.63 r_work: 0.2979 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35790 Z= 0.145 Angle : 0.536 10.034 48855 Z= 0.270 Chirality : 0.043 0.213 5667 Planarity : 0.004 0.092 6189 Dihedral : 4.620 53.405 5973 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.89 % Allowed : 11.26 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % 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: 0.41 (0.13), residues: 4323 helix: 2.08 (0.20), residues: 717 sheet: 0.39 (0.14), residues: 1248 loop : -0.31 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 983 TYR 0.023 0.001 TYR A 904 PHE 0.042 0.001 PHE F 67 TRP 0.015 0.001 TRP E 50 HIS 0.004 0.001 HIS H 72 Details of bonding type rmsd covalent geometry : bond 0.00326 (35676) covalent geometry : angle 0.52075 (48567) SS BOND : bond 0.00083 ( 54) SS BOND : angle 0.48306 ( 108) hydrogen bonds : bond 0.03491 ( 1413) hydrogen bonds : angle 5.18257 ( 4029) link_BETA1-4 : bond 0.00242 ( 18) link_BETA1-4 : angle 1.04078 ( 54) link_NAG-ASN : bond 0.00515 ( 42) link_NAG-ASN : angle 2.46433 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8806 (m-80) cc_final: 0.8471 (m-80) REVERT: A 1017 GLU cc_start: 0.9051 (tt0) cc_final: 0.8795 (tm-30) REVERT: D 34 MET cc_start: 0.5323 (OUTLIER) cc_final: 0.4624 (mtp) REVERT: D 90 THR cc_start: 0.6390 (OUTLIER) cc_final: 0.6160 (m) REVERT: D 101 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6859 (m-30) REVERT: E 4 MET cc_start: 0.6052 (mtm) cc_final: 0.5316 (ptm) REVERT: G 4 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.5609 (ptm) REVERT: I 4 MET cc_start: 0.7145 (tpp) cc_final: 0.6318 (ttp) REVERT: F 34 MET cc_start: 0.5372 (OUTLIER) cc_final: 0.4822 (mtp) REVERT: F 90 THR cc_start: 0.6695 (OUTLIER) cc_final: 0.6476 (m) REVERT: F 101 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7010 (m-30) REVERT: H 34 MET cc_start: 0.4887 (OUTLIER) cc_final: 0.4472 (mmp) REVERT: H 67 PHE cc_start: 0.4387 (m-10) cc_final: 0.3696 (m-10) REVERT: H 82 MET cc_start: -0.0395 (mmm) cc_final: -0.1716 (mtp) REVERT: B 934 ILE cc_start: 0.8797 (mm) cc_final: 0.8563 (mp) outliers start: 34 outliers final: 19 residues processed: 112 average time/residue: 0.5914 time to fit residues: 82.4610 Evaluate side-chains 108 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 142 ARG Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 343 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 chunk 407 optimal weight: 3.9990 chunk 189 optimal weight: 30.0000 chunk 392 optimal weight: 6.9990 chunk 429 optimal weight: 2.9990 chunk 272 optimal weight: 30.0000 chunk 222 optimal weight: 30.0000 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 chunk 334 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.106604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062340 restraints weight = 111416.058| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.55 r_work: 0.2843 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 35790 Z= 0.384 Angle : 0.693 12.006 48855 Z= 0.348 Chirality : 0.048 0.193 5667 Planarity : 0.005 0.095 6189 Dihedral : 5.282 53.290 5973 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.89 % Allowed : 11.55 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % 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: 0.06 (0.13), residues: 4323 helix: 1.54 (0.19), residues: 753 sheet: 0.05 (0.14), residues: 1338 loop : -0.42 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 86 TYR 0.041 0.002 TYR A 904 PHE 0.040 0.002 PHE F 67 TRP 0.028 0.002 TRP I 50 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00867 (35676) covalent geometry : angle 0.67796 (48567) SS BOND : bond 0.00255 ( 54) SS BOND : angle 0.76545 ( 108) hydrogen bonds : bond 0.04553 ( 1413) hydrogen bonds : angle 5.64886 ( 4029) link_BETA1-4 : bond 0.00204 ( 18) link_BETA1-4 : angle 1.42526 ( 54) link_NAG-ASN : bond 0.00845 ( 42) link_NAG-ASN : angle 2.77659 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 1.252 Fit side-chains REVERT: A 449 TYR cc_start: 0.8783 (m-80) cc_final: 0.8461 (m-80) REVERT: A 1017 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8843 (tm-30) REVERT: D 34 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4577 (mtp) REVERT: D 90 THR cc_start: 0.6337 (OUTLIER) cc_final: 0.6123 (m) REVERT: E 4 MET cc_start: 0.6115 (mtm) cc_final: 0.5189 (ptm) REVERT: G 4 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.5984 (ptm) REVERT: I 4 MET cc_start: 0.7485 (tpp) cc_final: 0.6951 (ttp) REVERT: F 34 MET cc_start: 0.5067 (mmp) cc_final: 0.4542 (mtp) REVERT: F 90 THR cc_start: 0.6646 (OUTLIER) cc_final: 0.6446 (m) REVERT: F 101 ASP cc_start: 0.7738 (m-30) cc_final: 0.7405 (m-30) REVERT: H 67 PHE cc_start: 0.4400 (m-10) cc_final: 0.3848 (m-10) REVERT: H 82 MET cc_start: -0.0364 (mmm) cc_final: -0.1651 (mtp) REVERT: B 697 MET cc_start: 0.9396 (ptt) cc_final: 0.9094 (ptt) REVERT: C 298 GLU cc_start: 0.9165 (tt0) cc_final: 0.8592 (tp30) REVERT: C 1017 GLU cc_start: 0.9158 (tt0) cc_final: 0.8863 (tm-30) outliers start: 34 outliers final: 19 residues processed: 110 average time/residue: 0.5970 time to fit residues: 81.2072 Evaluate side-chains 98 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 213 optimal weight: 30.0000 chunk 270 optimal weight: 0.0970 chunk 360 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 293 optimal weight: 0.4980 chunk 169 optimal weight: 40.0000 chunk 182 optimal weight: 0.0020 chunk 44 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 498 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.139187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.092049 restraints weight = 69891.654| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 5.44 r_work: 0.2985 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35790 Z= 0.100 Angle : 0.546 10.236 48855 Z= 0.276 Chirality : 0.044 0.260 5667 Planarity : 0.004 0.108 6189 Dihedral : 4.856 53.225 5973 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.58 % Allowed : 11.86 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % 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: 0.33 (0.13), residues: 4323 helix: 1.91 (0.20), residues: 735 sheet: 0.29 (0.15), residues: 1185 loop : -0.31 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 86 TYR 0.020 0.001 TYR A 904 PHE 0.053 0.001 PHE F 67 TRP 0.021 0.001 TRP I 50 HIS 0.005 0.001 HIS H 72 Details of bonding type rmsd covalent geometry : bond 0.00214 (35676) covalent geometry : angle 0.53203 (48567) SS BOND : bond 0.00126 ( 54) SS BOND : angle 0.50392 ( 108) hydrogen bonds : bond 0.03478 ( 1413) hydrogen bonds : angle 5.30348 ( 4029) link_BETA1-4 : bond 0.00386 ( 18) link_BETA1-4 : angle 0.90062 ( 54) link_NAG-ASN : bond 0.00526 ( 42) link_NAG-ASN : angle 2.45894 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16022.02 seconds wall clock time: 272 minutes 19.19 seconds (16339.19 seconds total)