Starting phenix.real_space_refine on Mon Jul 6 11:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mjk_23876/07_2026/7mjk_23876.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjk_23876/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7mjk_23876/07_2026/7mjk_23876.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mjk_23876/07_2026/7mjk_23876.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mjk_23876/07_2026/7mjk_23876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjk_23876/07_2026/7mjk_23876.map" model { file = "/net/cci-nas-00/data/ceres_data/7mjk_23876/07_2026/7mjk_23876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjk_23876/07_2026/7mjk_23876.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 7.26, per 1000 atoms: 0.21 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: 2.33 Conformation dependent library (CDL) restraints added in 1.3 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: 1.49 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: 10.20 Time building geometry restraints manager: 3.24 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: 19220 17.87 - 35.75: 1252 35.75 - 53.62: 207 53.62 - 71.50: 61 71.50 - 89.37: 44 Dihedral angle restraints: 20784 sinusoidal: 8037 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 20781 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: 0.10 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 33.210 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.140 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 13.059 89.373 12444 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/Z covalent geometry : bond 0.00441 / 0.21 (35676) covalent geometry : angle 0.79201 / 0.42 (48567) SS BOND : bond 0.00246 / 0.17 ( 54) SS BOND : angle 1.22708 / 0.87 ( 108) hydrogen bonds : bond 0.13387 / 8.50 ( 1413) hydrogen bonds : angle 7.45334 / 5.12 ( 4029) link_BETA1-4 : bond 0.00649 / 0.41 ( 18) link_BETA1-4 : angle 1.46414 / 0.99 ( 54) link_NAG-ASN : bond 0.00720 / 0.37 ( 42) link_NAG-ASN : angle 3.35895 / 2.86 ( 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 : 1.325 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: 0.7787 time to fit residues: 261.9102 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 : 1.343 ------------------------------------------------------------------------------- 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... 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 = 0.4448 r_free = 0.4448 target = 0.120054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.078587 restraints weight = 134074.787| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 5.09 r_work: 0.2959 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35790 Z= 0.233 Angle : 0.640 10.324 48855 Z= 0.327 Chirality : 0.046 0.200 5667 Planarity : 0.005 0.077 6189 Dihedral : 4.871 22.752 4719 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.84 % Allowed : 5.81 % Favored : 93.35 % 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: -0.13 (0.12), residues: 4323 helix: 1.34 (0.20), residues: 678 sheet: 0.20 (0.14), residues: 1338 loop : -0.67 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 346 TYR 0.018 0.002 TYR C1067 PHE 0.023 0.002 PHE C 275 TRP 0.017 0.001 TRP A 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (35676) covalent geometry : angle 0.62417 / 0.32 (48567) SS BOND : bond 0.00186 / 0.13 ( 54) SS BOND : angle 0.79313 / 0.55 ( 108) hydrogen bonds : bond 0.04373 / 2.79 ( 1413) hydrogen bonds : angle 5.94768 / 4.05 ( 4029) link_BETA1-4 : bond 0.00491 / 0.31 ( 18) link_BETA1-4 : angle 1.30202 / 0.89 ( 54) link_NAG-ASN : bond 0.00589 / 0.33 ( 42) link_NAG-ASN : angle 2.67657 / 2.20 ( 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 171 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8328 (pmm150) cc_final: 0.8102 (pmm150) REVERT: A 449 TYR cc_start: 0.8953 (m-80) cc_final: 0.8693 (m-80) REVERT: D 82 MET cc_start: 0.1242 (mtp) cc_final: 0.1009 (mtt) REVERT: D 101 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6839 (m-30) REVERT: G 4 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6517 (ptm) REVERT: I 4 MET cc_start: 0.7086 (mmm) cc_final: 0.6746 (ttp) REVERT: F 89 ASP cc_start: 0.4402 (m-30) cc_final: 0.3969 (m-30) REVERT: F 101 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: H 34 MET cc_start: 0.5203 (OUTLIER) cc_final: 0.4829 (tpp) REVERT: B 214 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8280 (ptm-80) REVERT: B 390 LEU cc_start: 0.9131 (mt) cc_final: 0.8796 (tm) outliers start: 32 outliers final: 8 residues processed: 160 average time/residue: 0.7445 time to fit residues: 143.5748 Evaluate side-chains 118 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 394 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 chunk 316 optimal weight: 2.9990 chunk 412 optimal weight: 2.9990 chunk 393 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 907 ASN A1010 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN G 27 GLN I 27 GLN I 42 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 HIS H 81 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.108261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.064820 restraints weight = 113395.973| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 4.39 r_work: 0.2935 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 35790 Z= 0.213 Angle : 0.589 9.768 48855 Z= 0.300 Chirality : 0.044 0.195 5667 Planarity : 0.005 0.078 6189 Dihedral : 4.617 20.295 4713 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.31 % Allowed : 7.59 % Favored : 91.10 % 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: 0.13 (0.12), residues: 4323 helix: 1.76 (0.20), residues: 684 sheet: 0.28 (0.14), residues: 1320 loop : -0.50 (0.12), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.021 0.001 TYR A 904 PHE 0.018 0.001 PHE B 275 TRP 0.013 0.001 TRP B 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (35676) covalent geometry : angle 0.57436 / 0.30 (48567) SS BOND : bond 0.00118 / 0.08 ( 54) SS BOND : angle 0.65827 / 0.45 ( 108) hydrogen bonds : bond 0.04025 / 2.58 ( 1413) hydrogen bonds : angle 5.66658 / 3.84 ( 4029) link_BETA1-4 : bond 0.00200 / 0.13 ( 18) link_BETA1-4 : angle 1.06106 / 0.71 ( 54) link_NAG-ASN : bond 0.00541 / 0.29 ( 42) link_NAG-ASN : angle 2.59110 / 2.18 ( 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 170 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8800 (m-80) cc_final: 0.8463 (m-80) REVERT: D 82 MET cc_start: 0.1011 (mtp) cc_final: 0.0673 (mtt) REVERT: D 90 THR cc_start: 0.5668 (OUTLIER) cc_final: 0.5420 (m) REVERT: D 101 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6877 (m-30) REVERT: E 4 MET cc_start: 0.6298 (mtm) cc_final: 0.5895 (mtt) REVERT: E 24 ARG cc_start: 0.8600 (tpp-160) cc_final: 0.8231 (tpp80) REVERT: G 4 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.5781 (ptm) REVERT: I 4 MET cc_start: 0.6964 (mmm) cc_final: 0.6524 (ttp) REVERT: F 90 THR cc_start: 0.5719 (OUTLIER) cc_final: 0.5468 (m) REVERT: F 101 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7081 (m-30) REVERT: B 214 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8365 (ptm-80) REVERT: B 390 LEU cc_start: 0.9025 (mt) cc_final: 0.8694 (tm) REVERT: B 697 MET cc_start: 0.9089 (ptt) cc_final: 0.8848 (ptt) REVERT: C 697 MET cc_start: 0.9162 (ptt) cc_final: 0.8912 (ptt) outliers start: 50 outliers final: 7 residues processed: 155 average time/residue: 0.6465 time to fit residues: 123.9155 Evaluate side-chains 109 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 214 ARG Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 226 LEU 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: 0.9980 chunk 437 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 431 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 189 optimal weight: 30.0000 chunk 367 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 824 ASN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 HIS H 203 ASN B 824 ASN B 907 ASN B 957 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 907 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.108086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.061151 restraints weight = 109925.598| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 4.13 r_work: 0.2910 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 35790 Z= 0.294 Angle : 0.632 9.366 48855 Z= 0.320 Chirality : 0.046 0.190 5667 Planarity : 0.005 0.080 6189 Dihedral : 4.695 20.816 4713 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.83 % Allowed : 8.35 % Favored : 89.81 % 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 (0.13), residues: 4323 helix: 1.68 (0.20), residues: 699 sheet: 0.16 (0.14), residues: 1326 loop : -0.45 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 19 TYR 0.026 0.002 TYR A 904 PHE 0.024 0.002 PHE D 67 TRP 0.014 0.001 TRP C 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.29 (35676) covalent geometry : angle 0.61681 / 0.32 (48567) SS BOND : bond 0.00180 / 0.12 ( 54) SS BOND : angle 0.74558 / 0.51 ( 108) hydrogen bonds : bond 0.04317 / 2.77 ( 1413) hydrogen bonds : angle 5.66869 / 3.85 ( 4029) link_BETA1-4 : bond 0.00147 / 0.08 ( 18) link_BETA1-4 : angle 1.19229 / 0.79 ( 54) link_NAG-ASN : bond 0.00660 / 0.40 ( 42) link_NAG-ASN : angle 2.66155 / 2.21 ( 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 170 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 100 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8833 (m-80) cc_final: 0.8472 (m-80) REVERT: A 1017 GLU cc_start: 0.9081 (tt0) cc_final: 0.8811 (tm-30) REVERT: D 101 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7072 (m-30) REVERT: D 148 ASP cc_start: 0.6062 (m-30) cc_final: 0.5595 (t0) REVERT: G 4 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6099 (ptm) REVERT: F 66 ARG cc_start: 0.7121 (ptt180) cc_final: 0.6370 (ptm-80) REVERT: F 101 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7103 (m-30) REVERT: C 126 VAL cc_start: 0.7605 (OUTLIER) cc_final: 0.7400 (t) REVERT: C 298 GLU cc_start: 0.9192 (tt0) cc_final: 0.8561 (tp30) REVERT: C 697 MET cc_start: 0.9227 (ptt) cc_final: 0.9010 (ptt) outliers start: 70 outliers final: 20 residues processed: 149 average time/residue: 0.6931 time to fit residues: 126.2477 Evaluate side-chains 109 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 3 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 19 ARG 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 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 56 optimal weight: 0.9980 chunk 410 optimal weight: 0.9980 chunk 231 optimal weight: 0.0060 chunk 366 optimal weight: 0.6980 chunk 310 optimal weight: 0.6980 chunk 405 optimal weight: 0.8980 chunk 395 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** I 42 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.114053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071513 restraints weight = 109989.727| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.30 r_work: 0.2946 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35790 Z= 0.107 Angle : 0.534 9.910 48855 Z= 0.271 Chirality : 0.043 0.204 5667 Planarity : 0.004 0.080 6189 Dihedral : 4.367 20.024 4713 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.31 % Allowed : 9.24 % Favored : 89.45 % 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: 0.29 (0.13), residues: 4323 helix: 2.04 (0.20), residues: 699 sheet: 0.26 (0.14), residues: 1260 loop : -0.36 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 66 TYR 0.019 0.001 TYR C1067 PHE 0.016 0.001 PHE C 565 TRP 0.009 0.001 TRP H 107 HIS 0.004 0.001 HIS H 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (35676) covalent geometry : angle 0.51917 / 0.27 (48567) SS BOND : bond 0.00078 / 0.05 ( 54) SS BOND : angle 0.51379 / 0.35 ( 108) hydrogen bonds : bond 0.03510 / 2.27 ( 1413) hydrogen bonds : angle 5.39265 / 3.66 ( 4029) link_BETA1-4 : bond 0.00362 / 0.22 ( 18) link_BETA1-4 : angle 0.80749 / 0.54 ( 54) link_NAG-ASN : bond 0.00523 / 0.27 ( 42) link_NAG-ASN : angle 2.45667 / 2.10 ( 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 155 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 105 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8876 (m-80) cc_final: 0.8531 (m-80) REVERT: A 1017 GLU cc_start: 0.9115 (tt0) cc_final: 0.8823 (tm-30) REVERT: D 90 THR cc_start: 0.5957 (OUTLIER) cc_final: 0.5708 (m) REVERT: D 101 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: G 4 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.5932 (ptm) REVERT: I 4 MET cc_start: 0.7053 (tpp) cc_final: 0.6283 (ttp) REVERT: F 34 MET cc_start: 0.5396 (OUTLIER) cc_final: 0.5097 (mmt) REVERT: F 90 THR cc_start: 0.5912 (OUTLIER) cc_final: 0.5661 (m) REVERT: F 101 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7013 (m-30) REVERT: B 934 ILE cc_start: 0.8900 (mm) cc_final: 0.8664 (mp) REVERT: C 298 GLU cc_start: 0.9198 (tt0) cc_final: 0.8555 (tp30) REVERT: C 697 MET cc_start: 0.9229 (ptt) cc_final: 0.8999 (ptt) outliers start: 50 outliers final: 13 residues processed: 140 average time/residue: 0.6864 time to fit residues: 117.9235 Evaluate side-chains 104 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 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 E residue 70 ASP Chi-restraints excluded: chain G residue 4 MET 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 19 ARG 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: 2.9990 chunk 358 optimal weight: 0.6980 chunk 123 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 430 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** 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 = 0.4241 r_free = 0.4241 target = 0.108288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.060569 restraints weight = 110116.570| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.83 r_work: 0.2945 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 35790 Z= 0.209 Angle : 0.569 9.624 48855 Z= 0.288 Chirality : 0.044 0.194 5667 Planarity : 0.004 0.083 6189 Dihedral : 4.420 20.943 4713 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.13 % Allowed : 9.90 % Favored : 88.98 % 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: 0.35 (0.13), residues: 4323 helix: 2.03 (0.20), residues: 699 sheet: 0.20 (0.13), residues: 1401 loop : -0.27 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 983 TYR 0.026 0.001 TYR A 904 PHE 0.017 0.001 PHE C 898 TRP 0.014 0.001 TRP I 50 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (35676) covalent geometry : angle 0.55428 / 0.28 (48567) SS BOND : bond 0.00104 / 0.07 ( 54) SS BOND : angle 0.56789 / 0.39 ( 108) hydrogen bonds : bond 0.03888 / 2.50 ( 1413) hydrogen bonds : angle 5.40674 / 3.66 ( 4029) link_BETA1-4 : bond 0.00172 / 0.10 ( 18) link_BETA1-4 : angle 1.07212 / 0.71 ( 54) link_NAG-ASN : bond 0.00588 / 0.34 ( 42) link_NAG-ASN : angle 2.52852 / 2.13 ( 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 146 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8896 (m-80) cc_final: 0.8589 (m-80) REVERT: A 1017 GLU cc_start: 0.9061 (tt0) cc_final: 0.8806 (tm-30) REVERT: D 90 THR cc_start: 0.6098 (OUTLIER) cc_final: 0.5857 (m) REVERT: D 101 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: G 4 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.5885 (ptm) REVERT: I 4 MET cc_start: 0.7224 (tpp) cc_final: 0.6476 (ttp) REVERT: F 19 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6898 (mmp80) REVERT: F 34 MET cc_start: 0.5295 (OUTLIER) cc_final: 0.4605 (mtp) REVERT: F 90 THR cc_start: 0.5788 (OUTLIER) cc_final: 0.5540 (m) REVERT: F 101 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7097 (m-30) REVERT: C 298 GLU cc_start: 0.9088 (tt0) cc_final: 0.8531 (tp30) outliers start: 43 outliers final: 15 residues processed: 136 average time/residue: 0.6783 time to fit residues: 113.7461 Evaluate side-chains 109 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 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 163 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 19 ARG 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 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 878 LEU 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: 7.9990 chunk 394 optimal weight: 2.9990 chunk 372 optimal weight: 0.8980 chunk 181 optimal weight: 20.0000 chunk 305 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 chunk 416 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 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 = 0.113568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068067 restraints weight = 109838.930| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.54 r_work: 0.2976 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35790 Z= 0.163 Angle : 0.544 10.119 48855 Z= 0.274 Chirality : 0.043 0.196 5667 Planarity : 0.004 0.084 6189 Dihedral : 4.325 20.242 4713 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.07 % Allowed : 10.60 % Favored : 88.32 % 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: 0.40 (0.13), residues: 4323 helix: 2.15 (0.20), residues: 699 sheet: 0.28 (0.14), residues: 1293 loop : -0.27 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 983 TYR 0.024 0.001 TYR A 904 PHE 0.024 0.001 PHE F 67 TRP 0.011 0.001 TRP H 107 HIS 0.004 0.001 HIS H 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (35676) covalent geometry : angle 0.52952 / 0.27 (48567) SS BOND : bond 0.00068 / 0.04 ( 54) SS BOND : angle 0.50382 / 0.35 ( 108) hydrogen bonds : bond 0.03629 / 2.34 ( 1413) hydrogen bonds : angle 5.30814 / 3.60 ( 4029) link_BETA1-4 : bond 0.00261 / 0.16 ( 18) link_BETA1-4 : angle 0.88181 / 0.58 ( 54) link_NAG-ASN : bond 0.00528 / 0.28 ( 42) link_NAG-ASN : angle 2.46344 / 2.10 ( 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 138 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8879 (m-80) cc_final: 0.8558 (m-80) REVERT: A 1017 GLU cc_start: 0.9060 (tt0) cc_final: 0.8785 (tm-30) REVERT: D 34 MET cc_start: 0.5300 (OUTLIER) cc_final: 0.4869 (mtt) REVERT: D 90 THR cc_start: 0.6401 (OUTLIER) cc_final: 0.6159 (m) REVERT: D 101 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6917 (m-30) REVERT: G 4 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.5188 (ptm) REVERT: I 4 MET cc_start: 0.6974 (tpp) cc_final: 0.6057 (ttp) REVERT: F 34 MET cc_start: 0.5258 (OUTLIER) cc_final: 0.4641 (mtp) REVERT: F 90 THR cc_start: 0.5903 (OUTLIER) cc_final: 0.5646 (m) REVERT: F 101 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: B 934 ILE cc_start: 0.8894 (mm) cc_final: 0.8612 (mp) REVERT: C 298 GLU cc_start: 0.9089 (tt0) cc_final: 0.8517 (tp30) REVERT: C 697 MET cc_start: 0.9376 (ptt) cc_final: 0.9101 (ptt) outliers start: 41 outliers final: 17 residues processed: 129 average time/residue: 0.6734 time to fit residues: 107.1780 Evaluate side-chains 110 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 E residue 4 MET 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 19 ARG 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 62 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 878 LEU 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: 0.6980 chunk 437 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 296 optimal weight: 3.9990 chunk 427 optimal weight: 0.5980 chunk 236 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 309 optimal weight: 0.4980 chunk 424 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.114149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071923 restraints weight = 109960.906| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 4.06 r_work: 0.2984 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35790 Z= 0.103 Angle : 0.515 10.066 48855 Z= 0.260 Chirality : 0.043 0.215 5667 Planarity : 0.004 0.086 6189 Dihedral : 4.164 20.223 4713 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.92 % Allowed : 11.05 % Favored : 88.03 % 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: 0.49 (0.13), residues: 4323 helix: 2.33 (0.20), residues: 699 sheet: 0.39 (0.14), residues: 1239 loop : -0.27 (0.13), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 983 TYR 0.018 0.001 TYR B1067 PHE 0.022 0.001 PHE C 565 TRP 0.011 0.001 TRP H 107 HIS 0.004 0.001 HIS H 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (35676) covalent geometry : angle 0.50098 / 0.26 (48567) SS BOND : bond 0.00094 / 0.07 ( 54) SS BOND : angle 0.46917 / 0.32 ( 108) hydrogen bonds : bond 0.03325 / 2.15 ( 1413) hydrogen bonds : angle 5.13645 / 3.48 ( 4029) link_BETA1-4 : bond 0.00340 / 0.21 ( 18) link_BETA1-4 : angle 0.83025 / 0.55 ( 54) link_NAG-ASN : bond 0.00509 / 0.26 ( 42) link_NAG-ASN : angle 2.39093 / 2.06 ( 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 126 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8917 (m-80) cc_final: 0.8640 (m-80) REVERT: A 1017 GLU cc_start: 0.9075 (tt0) cc_final: 0.8814 (tm-30) REVERT: D 34 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4486 (mtp) REVERT: D 90 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6342 (m) REVERT: D 101 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6881 (m-30) REVERT: E 4 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5003 (ptm) REVERT: G 4 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.5498 (ptm) REVERT: I 4 MET cc_start: 0.7071 (tpp) cc_final: 0.6168 (ttm) REVERT: F 34 MET cc_start: 0.5193 (OUTLIER) cc_final: 0.4626 (mtp) REVERT: F 90 THR cc_start: 0.5899 (OUTLIER) cc_final: 0.5649 (m) REVERT: F 101 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: B 934 ILE cc_start: 0.8774 (mm) cc_final: 0.8559 (mp) REVERT: C 697 MET cc_start: 0.9358 (ptt) cc_final: 0.9118 (ptt) outliers start: 35 outliers final: 15 residues processed: 114 average time/residue: 0.6067 time to fit residues: 85.2294 Evaluate side-chains 111 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 4 MET Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain G residue 4 MET 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 19 ARG 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 902 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 452 LEU 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: 0.9980 chunk 437 optimal weight: 5.9990 chunk 330 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 402 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 269 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 HIS H 76 ASN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.108305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.061906 restraints weight = 110675.894| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.73 r_work: 0.2967 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35790 Z= 0.188 Angle : 0.549 9.745 48855 Z= 0.277 Chirality : 0.044 0.195 5667 Planarity : 0.004 0.086 6189 Dihedral : 4.247 20.591 4713 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.84 % Allowed : 11.23 % Favored : 87.93 % 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: 0.45 (0.13), residues: 4323 helix: 2.08 (0.20), residues: 717 sheet: 0.41 (0.14), residues: 1245 loop : -0.28 (0.13), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.024 0.001 TYR A 904 PHE 0.036 0.001 PHE F 67 TRP 0.023 0.001 TRP I 50 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (35676) covalent geometry : angle 0.53441 / 0.27 (48567) SS BOND : bond 0.00103 / 0.07 ( 54) SS BOND : angle 0.50554 / 0.35 ( 108) hydrogen bonds : bond 0.03678 / 2.38 ( 1413) hydrogen bonds : angle 5.22043 / 3.53 ( 4029) link_BETA1-4 : bond 0.00193 / 0.12 ( 18) link_BETA1-4 : angle 0.99054 / 0.65 ( 54) link_NAG-ASN : bond 0.00540 / 0.30 ( 42) link_NAG-ASN : angle 2.43562 / 2.08 ( 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 126 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8942 (m-80) cc_final: 0.8658 (m-80) REVERT: A 1017 GLU cc_start: 0.9056 (tt0) cc_final: 0.8794 (tm-30) REVERT: D 34 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4526 (mtp) REVERT: D 90 THR cc_start: 0.6681 (OUTLIER) cc_final: 0.6462 (m) REVERT: D 101 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: E 4 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5194 (ptm) REVERT: G 4 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.5728 (ptm) REVERT: I 4 MET cc_start: 0.7131 (tpp) cc_final: 0.6324 (ttp) REVERT: F 34 MET cc_start: 0.5154 (OUTLIER) cc_final: 0.4613 (mtp) REVERT: F 90 THR cc_start: 0.6055 (OUTLIER) cc_final: 0.5820 (m) REVERT: F 101 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: B 934 ILE cc_start: 0.8877 (mm) cc_final: 0.8631 (mp) REVERT: C 298 GLU cc_start: 0.9106 (tt0) cc_final: 0.8546 (tp30) REVERT: C 697 MET cc_start: 0.9376 (ptt) cc_final: 0.9123 (ptt) outliers start: 32 outliers final: 18 residues processed: 116 average time/residue: 0.6380 time to fit residues: 91.6566 Evaluate side-chains 112 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 4 MET Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 163 VAL 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 19 ARG 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 62 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 452 LEU 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: 6.9990 chunk 275 optimal weight: 8.9990 chunk 407 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 392 optimal weight: 5.9990 chunk 429 optimal weight: 0.5980 chunk 272 optimal weight: 20.0000 chunk 222 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 126 optimal weight: 30.0000 chunk 334 optimal weight: 20.0000 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN ** 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** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 HIS ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.107126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.059772 restraints weight = 111095.640| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.60 r_work: 0.2917 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 35790 Z= 0.309 Angle : 0.636 9.070 48855 Z= 0.320 Chirality : 0.046 0.263 5667 Planarity : 0.005 0.090 6189 Dihedral : 4.627 22.118 4713 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.84 % Allowed : 11.36 % Favored : 87.80 % 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: 0.17 (0.13), residues: 4323 helix: 1.64 (0.19), residues: 753 sheet: 0.12 (0.14), residues: 1365 loop : -0.36 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 24 TYR 0.034 0.002 TYR A 904 PHE 0.033 0.002 PHE F 67 TRP 0.022 0.002 TRP I 50 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.31 (35676) covalent geometry : angle 0.62214 / 0.32 (48567) SS BOND : bond 0.00206 / 0.14 ( 54) SS BOND : angle 0.69347 / 0.48 ( 108) hydrogen bonds : bond 0.04352 / 2.80 ( 1413) hydrogen bonds : angle 5.57926 / 3.78 ( 4029) link_BETA1-4 : bond 0.00130 / 0.08 ( 18) link_BETA1-4 : angle 1.19212 / 0.77 ( 54) link_NAG-ASN : bond 0.00714 / 0.44 ( 42) link_NAG-ASN : angle 2.60646 / 2.18 ( 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 113 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8908 (m-80) cc_final: 0.8628 (m-80) REVERT: A 1017 GLU cc_start: 0.9116 (tt0) cc_final: 0.8807 (tm-30) REVERT: D 34 MET cc_start: 0.5180 (mmp) cc_final: 0.4597 (mtp) REVERT: D 90 THR cc_start: 0.6739 (OUTLIER) cc_final: 0.6529 (m) REVERT: D 101 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: E 4 MET cc_start: 0.5983 (OUTLIER) cc_final: 0.5192 (ptm) REVERT: G 4 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6314 (mtt) REVERT: I 4 MET cc_start: 0.7324 (tpp) cc_final: 0.6682 (ttp) REVERT: F 34 MET cc_start: 0.5069 (OUTLIER) cc_final: 0.4561 (mtp) REVERT: F 90 THR cc_start: 0.6244 (OUTLIER) cc_final: 0.6017 (m) REVERT: H 34 MET cc_start: 0.4720 (mmp) cc_final: 0.4345 (mtp) REVERT: C 298 GLU cc_start: 0.9108 (tt0) cc_final: 0.8574 (tp30) REVERT: C 697 MET cc_start: 0.9314 (ptt) cc_final: 0.8980 (ptt) REVERT: C 1017 GLU cc_start: 0.9090 (tt0) cc_final: 0.8826 (tm-30) outliers start: 32 outliers final: 17 residues processed: 107 average time/residue: 0.5675 time to fit residues: 75.5135 Evaluate side-chains 97 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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 4 MET Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain G residue 4 MET 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 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 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 452 LEU 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: 0.9980 chunk 270 optimal weight: 0.0470 chunk 360 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 293 optimal weight: 0.5980 chunk 169 optimal weight: 40.0000 chunk 182 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 76 ASN ** 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 ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.108758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.062025 restraints weight = 110632.720| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.69 r_work: 0.2988 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35790 Z= 0.104 Angle : 0.533 10.077 48855 Z= 0.269 Chirality : 0.043 0.207 5667 Planarity : 0.004 0.106 6189 Dihedral : 4.282 20.804 4713 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.50 % Allowed : 11.70 % Favored : 87.80 % 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: 2.13 (0.20), residues: 717 sheet: 0.30 (0.14), residues: 1215 loop : -0.27 (0.13), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.021 0.001 TYR A 904 PHE 0.029 0.001 PHE F 67 TRP 0.022 0.001 TRP I 50 HIS 0.004 0.001 HIS H 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (35676) covalent geometry : angle 0.51932 / 0.27 (48567) SS BOND : bond 0.00134 / 0.10 ( 54) SS BOND : angle 0.49924 / 0.35 ( 108) hydrogen bonds : bond 0.03464 / 2.24 ( 1413) hydrogen bonds : angle 5.26089 / 3.56 ( 4029) link_BETA1-4 : bond 0.00385 / 0.24 ( 18) link_BETA1-4 : angle 0.81205 / 0.55 ( 54) link_NAG-ASN : bond 0.00514 / 0.26 ( 42) link_NAG-ASN : angle 2.40402 / 2.07 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15928.97 seconds wall clock time: 271 minutes 31.49 seconds (16291.49 seconds total)