Starting phenix.real_space_refine on Sat Dec 28 11:20:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpv_34945/12_2024/8hpv_34945.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpv_34945/12_2024/8hpv_34945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpv_34945/12_2024/8hpv_34945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpv_34945/12_2024/8hpv_34945.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpv_34945/12_2024/8hpv_34945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpv_34945/12_2024/8hpv_34945.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9426 atoms to isotropic. 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 189 5.16 5 C 28278 2.51 5 N 7455 2.21 5 O 8718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44640 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8131 Classifications: {'peptide': 1040} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "H" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8131 Classifications: {'peptide': 1040} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "Q" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "C" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8131 Classifications: {'peptide': 1040} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "J" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "R" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "S" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 20.00, per 1000 atoms: 0.45 Number of scatterers: 44640 At special positions: 0 Unit cell: (235.4, 223.416, 249.952, 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 189 16.00 O 8718 8.00 N 7455 7.00 C 28278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.04 Simple disulfide: pdb=" SG CYS M 149 " - pdb=" SG CYS M 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 225 " - pdb=" SG CYS N 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS H 231 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 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=2.05 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 155 " - pdb=" SG CYS P 211 " distance=2.03 Simple disulfide: pdb=" SG CYS P 231 " - pdb=" SG CYS Q 215 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 135 " - pdb=" SG CYS Q 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 149 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS I 231 " - pdb=" SG CYS J 215 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.04 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 95 " distance=2.04 Simple disulfide: pdb=" SG CYS R 149 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS R 225 " - pdb=" SG CYS S 216 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 136 " - pdb=" SG CYS S 196 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG D 1 " - " ASN A 343 " " NAG G 1 " - " ASN B 343 " " NAG K 1 " - " ASN C 343 " Time building additional restraints: 8.00 Conformation dependent library (CDL) restraints added in 4.4 seconds 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10758 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 109 sheets defined 17.0% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.31 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 364 through 371 removed outlier: 4.068A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.928A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.078A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.879A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.554A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.502A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.533A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.042A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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: 4.268A 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 'M' and resid 86 through 90 Processing helix chain 'M' and resid 165 through 167 No H-bonds generated for 'chain 'M' and resid 165 through 167' Processing helix chain 'M' and resid 194 through 199 removed outlier: 4.035A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 184 through 191 removed outlier: 3.880A pdb=" N LYS N 190 " --> pdb=" O ALA N 186 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS N 191 " --> pdb=" O ASP N 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.514A pdb=" N LEU H 204 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 184 through 189 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: 3.636A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.550A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.016A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.513A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.313A 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 removed outlier: 3.951A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.778A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.619A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.572A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.008A 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 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.510A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.251A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.651A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 67 No H-bonds generated for 'chain 'P' and resid 65 through 67' Processing helix chain 'P' and resid 88 through 92 removed outlier: 3.973A pdb=" N THR P 92 " --> pdb=" O PRO P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 173 No H-bonds generated for 'chain 'P' and resid 171 through 173' Processing helix chain 'P' and resid 200 through 204 Processing helix chain 'Q' and resid 30 through 34 removed outlier: 3.719A pdb=" N LEU Q 34 " --> pdb=" O SER Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 84 removed outlier: 3.946A pdb=" N PHE Q 84 " --> pdb=" O PRO Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 188 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.151A pdb=" N GLY E 199 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 185 through 191 removed outlier: 3.612A pdb=" N LYS F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.509A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.862A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.658A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.987A 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 removed outlier: 3.805A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.529A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.839A 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 885 removed outlier: 3.548A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.056A 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: 3.542A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.420A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 88 through 92 removed outlier: 4.062A pdb=" N THR I 92 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 200 through 204 Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.951A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.567A pdb=" N SER R 31 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN R 32 " --> pdb=" O VAL R 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 28 through 32' Processing helix chain 'R' and resid 86 through 90 removed outlier: 3.775A pdb=" N THR R 90 " --> pdb=" O ALA R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 167 No H-bonds generated for 'chain 'R' and resid 165 through 167' Processing helix chain 'R' and resid 194 through 199 removed outlier: 3.628A pdb=" N GLY R 199 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 83 removed outlier: 4.124A pdb=" N PHE S 83 " --> pdb=" O PRO S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 128 Processing helix chain 'S' and resid 185 through 190 removed outlier: 3.729A pdb=" N LYS S 190 " --> pdb=" O ALA S 186 " (cutoff:3.500A) 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: 7.997A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.990A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.948A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.663A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.505A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.013A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.748A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.997A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.725A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.899A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 11.663A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.505A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.212A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.552A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.090A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.833A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.833A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.627A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.384A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.097A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.935A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.935A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER M 186 " --> pdb=" O VAL M 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 160 through 163 Processing sheet with id=AC5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.382A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.820A pdb=" N GLN N 90 " --> pdb=" O SER N 99 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER N 99 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 116 through 120 removed outlier: 6.080A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER N 176 " --> pdb=" O THR N 166 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 146 through 152 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.764A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.263A pdb=" N PHE H 101 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N PHE H 115 " --> pdb=" O PHE H 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 135 through 139 Processing sheet with id=AD5, first strand: chain 'H' and resid 135 through 139 Processing sheet with id=AD6, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.809A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.354A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.861A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 146 through 151 Processing sheet with id=AE2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AE3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.184A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.177A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.634A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.977A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.742A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.856A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.708A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.633A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.637A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.633A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.099A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AF3, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AF4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AF6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.233A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.682A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.682A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.466A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.434A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AG3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG4, first strand: chain 'P' and resid 59 through 61 removed outlier: 6.606A pdb=" N TRP P 38 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU P 52 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL P 36 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE P 101 " --> pdb=" O TRP P 114 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP P 114 " --> pdb=" O PHE P 101 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 59 through 61 removed outlier: 6.606A pdb=" N TRP P 38 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU P 52 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL P 36 " --> pdb=" O LEU P 52 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 135 through 139 removed outlier: 6.494A pdb=" N TYR P 191 " --> pdb=" O ASP P 159 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 135 through 139 removed outlier: 6.494A pdb=" N TYR P 191 " --> pdb=" O ASP P 159 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER P 192 " --> pdb=" O VAL P 184 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 166 through 169 removed outlier: 3.899A pdb=" N TYR P 209 " --> pdb=" O VAL P 226 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AH1, first strand: chain 'Q' and resid 10 through 13 removed outlier: 6.675A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 115 through 119 Processing sheet with id=AH3, first strand: chain 'Q' and resid 154 through 155 Processing sheet with id=AH4, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AH5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLY E 10 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR E 33 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 129 through 133 removed outlier: 6.104A pdb=" N TYR E 185 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 129 through 133 removed outlier: 6.104A pdb=" N TYR E 185 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 160 through 163 Processing sheet with id=AH9, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AI1, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.153A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.711A pdb=" N GLN F 90 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER F 99 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 116 through 120 removed outlier: 6.302A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 156 through 157 removed outlier: 4.378A pdb=" N TRP F 150 " --> pdb=" O GLN F 157 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.206A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.644A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.389A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.945A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.653A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.865A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.938A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.615A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AJ2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AJ3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AJ4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.179A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.661A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.661A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.593A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AJ9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AK1, first strand: chain 'I' and resid 59 through 61 removed outlier: 5.151A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'I' and resid 59 through 61 removed outlier: 5.151A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'I' and resid 135 through 139 removed outlier: 6.414A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I' and resid 135 through 139 removed outlier: 6.414A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.759A pdb=" N TYR I 209 " --> pdb=" O VAL I 226 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AK7, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.494A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'J' and resid 115 through 119 removed outlier: 5.823A pdb=" N TYR J 174 " --> pdb=" O ASN J 139 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'J' and resid 154 through 155 Processing sheet with id=AL1, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AL2, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.164A pdb=" N GLY R 10 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR R 33 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.164A pdb=" N GLY R 10 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE R 111 " --> pdb=" O ARG R 97 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'R' and resid 129 through 133 removed outlier: 6.071A pdb=" N TYR R 185 " --> pdb=" O ASP R 153 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'R' and resid 129 through 133 removed outlier: 6.071A pdb=" N TYR R 185 " --> pdb=" O ASP R 153 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER R 186 " --> pdb=" O VAL R 178 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'R' and resid 160 through 163 Processing sheet with id=AL7, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.610A pdb=" N ASP S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'S' and resid 10 through 12 removed outlier: 7.023A pdb=" N LEU S 33 " --> pdb=" O SER S 49 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER S 49 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'S' and resid 116 through 120 removed outlier: 6.262A pdb=" N TYR S 175 " --> pdb=" O ASN S 140 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER S 176 " --> pdb=" O THR S 166 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'S' and resid 146 through 152 2025 hydrogen bonds defined for protein. 5328 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: 20.69 Time building geometry restraints manager: 9.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 1 1.19 - 1.35: 14381 1.35 - 1.51: 13792 1.51 - 1.67: 17267 1.67 - 1.83: 234 Bond restraints: 45675 Sorted by residual: bond pdb=" CG PRO S 44 " pdb=" CD PRO S 44 " ideal model delta sigma weight residual 1.503 1.027 0.476 3.40e-02 8.65e+02 1.96e+02 bond pdb=" N PRO S 44 " pdb=" CD PRO S 44 " ideal model delta sigma weight residual 1.473 1.565 -0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" CB PRO R 158 " pdb=" CG PRO R 158 " ideal model delta sigma weight residual 1.506 1.646 -0.140 3.90e-02 6.57e+02 1.29e+01 bond pdb=" CB PRO S 44 " pdb=" CG PRO S 44 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.75e+00 bond pdb=" CB PRO I 164 " pdb=" CG PRO I 164 " ideal model delta sigma weight residual 1.506 1.607 -0.101 3.90e-02 6.57e+02 6.65e+00 ... (remaining 45670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.53: 62091 4.53 - 9.05: 67 9.05 - 13.58: 6 13.58 - 18.11: 4 18.11 - 22.64: 1 Bond angle restraints: 62169 Sorted by residual: angle pdb=" N PRO S 44 " pdb=" CD PRO S 44 " pdb=" CG PRO S 44 " ideal model delta sigma weight residual 103.20 80.56 22.64 1.50e+00 4.44e-01 2.28e+02 angle pdb=" CA PRO S 44 " pdb=" N PRO S 44 " pdb=" CD PRO S 44 " ideal model delta sigma weight residual 112.00 96.43 15.57 1.40e+00 5.10e-01 1.24e+02 angle pdb=" CA PRO I 164 " pdb=" N PRO I 164 " pdb=" CD PRO I 164 " ideal model delta sigma weight residual 111.50 99.34 12.16 1.40e+00 5.10e-01 7.54e+01 angle pdb=" CA PRO S 44 " pdb=" CB PRO S 44 " pdb=" CG PRO S 44 " ideal model delta sigma weight residual 104.50 88.03 16.47 1.90e+00 2.77e-01 7.51e+01 angle pdb=" CA PRO R 158 " pdb=" N PRO R 158 " pdb=" CD PRO R 158 " ideal model delta sigma weight residual 111.50 100.39 11.11 1.40e+00 5.10e-01 6.29e+01 ... (remaining 62164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 25258 17.83 - 35.66: 1735 35.66 - 53.50: 284 53.50 - 71.33: 84 71.33 - 89.16: 62 Dihedral angle restraints: 27423 sinusoidal: 10677 harmonic: 16746 Sorted by residual: dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual -86.00 -3.08 -82.92 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual -86.00 -7.19 -78.81 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CA ASP I 116 " pdb=" C ASP I 116 " pdb=" N PRO I 117 " pdb=" CA PRO I 117 " ideal model delta harmonic sigma weight residual 180.00 -136.51 -43.49 0 5.00e+00 4.00e-02 7.57e+01 ... (remaining 27420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 5009 0.043 - 0.086: 1445 0.086 - 0.130: 573 0.130 - 0.173: 38 0.173 - 0.216: 9 Chirality restraints: 7074 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.84e+00 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.30e+00 chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 7071 not shown) Planarity restraints: 8022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " -0.084 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO A 82 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 163 " 0.088 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO I 164 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO I 164 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO I 164 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 43 " -0.084 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO S 44 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO S 44 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO S 44 " -0.059 5.00e-02 4.00e+02 ... (remaining 8019 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 707 2.68 - 3.23: 40007 3.23 - 3.79: 65994 3.79 - 4.34: 92152 4.34 - 4.90: 152954 Nonbonded interactions: 351814 Sorted by model distance: nonbonded pdb=" OG SER Q 163 " pdb=" OG SER Q 177 " model vdw 2.124 3.040 nonbonded pdb=" OG SER L 163 " pdb=" OG SER L 177 " model vdw 2.137 3.040 nonbonded pdb=" OG SER J 163 " pdb=" OG SER J 177 " model vdw 2.143 3.040 nonbonded pdb=" OD2 ASP F 172 " pdb=" OG1 THR F 174 " model vdw 2.166 3.040 nonbonded pdb=" OD2 ASP N 172 " pdb=" OG1 THR N 174 " model vdw 2.168 3.040 ... (remaining 351809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'Q' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.030 Extract box with map and model: 1.470 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 86.020 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 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 0.476 45675 Z= 0.294 Angle : 0.675 22.637 62169 Z= 0.381 Chirality : 0.046 0.216 7074 Planarity : 0.006 0.128 8019 Dihedral : 13.097 89.158 16449 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.04 % Allowed : 0.16 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.31 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.11), residues: 5703 helix: 1.31 (0.20), residues: 727 sheet: 1.23 (0.12), residues: 1890 loop : -0.82 (0.11), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 886 HIS 0.007 0.001 HIS H 99 PHE 0.032 0.002 PHE B 906 TYR 0.023 0.001 TYR I 110 ARG 0.006 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 277 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 108 LYS cc_start: 0.2989 (ttpp) cc_final: 0.2785 (ptmm) REVERT: S 209 LYS cc_start: 0.0093 (tptm) cc_final: -0.0915 (tptp) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 1.1449 time to fit residues: 404.1527 Evaluate side-chains 202 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 483 optimal weight: 3.9990 chunk 434 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 292 optimal weight: 0.0030 chunk 232 optimal weight: 0.6980 chunk 449 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 520 optimal weight: 0.2980 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 450 ASN N 139 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN F 34 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 422 ASN C 901 GLN I 103 HIS ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 201 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 45675 Z= 0.171 Angle : 0.564 10.386 62169 Z= 0.297 Chirality : 0.045 0.192 7074 Planarity : 0.005 0.084 8019 Dihedral : 4.486 38.168 6312 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.78 % Allowed : 4.93 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.31 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.11), residues: 5703 helix: 1.64 (0.20), residues: 725 sheet: 1.25 (0.12), residues: 1953 loop : -0.72 (0.11), residues: 3025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 886 HIS 0.008 0.001 HIS C 207 PHE 0.023 0.001 PHE B 541 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG Q 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: A 569 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8290 (mm) REVERT: A 725 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: N 100 PHE cc_start: 0.3560 (OUTLIER) cc_final: 0.1961 (t80) REVERT: C 314 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: I 103 HIS cc_start: 0.2507 (t-90) cc_final: 0.1847 (t-170) outliers start: 39 outliers final: 10 residues processed: 252 average time/residue: 1.0961 time to fit residues: 354.0361 Evaluate side-chains 209 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 289 optimal weight: 2.9990 chunk 161 optimal weight: 0.3980 chunk 433 optimal weight: 0.1980 chunk 354 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 521 optimal weight: 9.9990 chunk 563 optimal weight: 0.8980 chunk 464 optimal weight: 0.7980 chunk 516 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 418 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS J 125 GLN ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45675 Z= 0.180 Angle : 0.546 9.877 62169 Z= 0.288 Chirality : 0.044 0.187 7074 Planarity : 0.004 0.065 8019 Dihedral : 4.357 34.523 6312 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.89 % Allowed : 7.14 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.31 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 5703 helix: 1.83 (0.20), residues: 720 sheet: 1.29 (0.12), residues: 1936 loop : -0.68 (0.11), residues: 3047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 114 HIS 0.008 0.001 HIS C 207 PHE 0.022 0.001 PHE C 157 TYR 0.023 0.001 TYR B 380 ARG 0.014 0.000 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 3.685 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: A 569 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8304 (mm) REVERT: A 725 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: M 34 MET cc_start: 0.3942 (OUTLIER) cc_final: 0.3641 (mmp) REVERT: N 100 PHE cc_start: 0.3430 (OUTLIER) cc_final: 0.1933 (t80) REVERT: C 314 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: I 103 HIS cc_start: 0.2186 (t-90) cc_final: 0.1805 (t-170) outliers start: 45 outliers final: 14 residues processed: 236 average time/residue: 1.0793 time to fit residues: 329.6948 Evaluate side-chains 206 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 515 optimal weight: 20.0000 chunk 391 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 350 optimal weight: 20.0000 chunk 523 optimal weight: 0.0670 chunk 553 optimal weight: 20.0000 chunk 273 optimal weight: 3.9990 chunk 495 optimal weight: 8.9990 chunk 149 optimal weight: 30.0000 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 245 HIS A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 501 ASN J 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 45675 Z= 0.417 Angle : 0.670 10.696 62169 Z= 0.357 Chirality : 0.050 0.200 7074 Planarity : 0.005 0.069 8019 Dihedral : 4.898 31.206 6312 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.61 % Allowed : 8.85 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.31 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.11), residues: 5703 helix: 1.25 (0.19), residues: 730 sheet: 1.14 (0.12), residues: 1934 loop : -0.91 (0.11), residues: 3039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 104 HIS 0.010 0.001 HIS C 207 PHE 0.027 0.002 PHE C 157 TYR 0.026 0.002 TYR C 380 ARG 0.007 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 205 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8333 (mm) REVERT: A 725 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: N 100 PHE cc_start: 0.3699 (OUTLIER) cc_final: 0.2210 (t80) REVERT: H 24 PHE cc_start: 0.4557 (p90) cc_final: 0.4330 (p90) REVERT: H 87 MET cc_start: 0.3521 (mmp) cc_final: 0.3316 (mmm) REVERT: B 239 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: P 165 VAL cc_start: 0.1694 (OUTLIER) cc_final: 0.1450 (t) REVERT: Q 92 PHE cc_start: 0.4563 (m-80) cc_final: 0.4120 (m-80) REVERT: Q 178 SER cc_start: -0.0007 (OUTLIER) cc_final: -0.0296 (t) REVERT: E 117 MET cc_start: 0.1062 (OUTLIER) cc_final: 0.0243 (ppp) REVERT: C 1010 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7646 (pt0) REVERT: I 103 HIS cc_start: 0.2538 (t-90) cc_final: 0.2066 (t-170) outliers start: 81 outliers final: 36 residues processed: 261 average time/residue: 1.0294 time to fit residues: 351.3271 Evaluate side-chains 235 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 178 SER Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain I residue 15 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 461 optimal weight: 0.3980 chunk 314 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 412 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 chunk 472 optimal weight: 0.6980 chunk 382 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 282 optimal weight: 0.8980 chunk 497 optimal weight: 0.0770 chunk 139 optimal weight: 20.0000 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 125 ASN B 992 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 207 HIS C1011 GLN J 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 45675 Z= 0.163 Angle : 0.536 9.168 62169 Z= 0.284 Chirality : 0.044 0.193 7074 Planarity : 0.004 0.063 8019 Dihedral : 4.437 28.287 6312 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.39 % Allowed : 9.84 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.11), residues: 5703 helix: 1.81 (0.20), residues: 713 sheet: 1.21 (0.12), residues: 1951 loop : -0.75 (0.11), residues: 3039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 353 HIS 0.010 0.001 HIS C 207 PHE 0.025 0.001 PHE C 157 TYR 0.025 0.001 TYR I 110 ARG 0.004 0.000 ARG Q 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: A 740 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7708 (ttt) REVERT: N 100 PHE cc_start: 0.3505 (OUTLIER) cc_final: 0.2032 (t80) REVERT: P 165 VAL cc_start: 0.1677 (OUTLIER) cc_final: 0.1421 (t) REVERT: Q 178 SER cc_start: -0.0296 (OUTLIER) cc_final: -0.0513 (t) REVERT: I 87 MET cc_start: 0.0162 (OUTLIER) cc_final: -0.1516 (tpp) REVERT: J 79 LEU cc_start: 0.3738 (OUTLIER) cc_final: 0.3536 (pp) outliers start: 70 outliers final: 21 residues processed: 261 average time/residue: 1.0646 time to fit residues: 360.1555 Evaluate side-chains 214 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 178 SER Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 162 GLU Chi-restraints excluded: chain S residue 15 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 186 optimal weight: 0.6980 chunk 498 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 325 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 554 optimal weight: 4.9990 chunk 460 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 291 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 GLN C 207 HIS J 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 45675 Z= 0.261 Angle : 0.581 12.019 62169 Z= 0.307 Chirality : 0.046 0.191 7074 Planarity : 0.005 0.068 8019 Dihedral : 4.541 27.604 6312 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.41 % Allowed : 10.87 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.11), residues: 5703 helix: 1.65 (0.20), residues: 732 sheet: 1.13 (0.12), residues: 1966 loop : -0.80 (0.11), residues: 3005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 38 HIS 0.010 0.001 HIS C 207 PHE 0.024 0.002 PHE C 157 TYR 0.022 0.002 TYR C 265 ARG 0.006 0.000 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 206 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: A 569 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8314 (mm) REVERT: N 100 PHE cc_start: 0.3541 (OUTLIER) cc_final: 0.2117 (t80) REVERT: B 740 MET cc_start: 0.7861 (ttt) cc_final: 0.7635 (ttt) REVERT: P 165 VAL cc_start: 0.1767 (OUTLIER) cc_final: 0.1539 (t) REVERT: Q 178 SER cc_start: -0.0162 (OUTLIER) cc_final: -0.0420 (t) REVERT: C 513 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7671 (mp) REVERT: I 87 MET cc_start: 0.0027 (OUTLIER) cc_final: -0.1543 (tpp) REVERT: I 103 HIS cc_start: 0.2915 (t-170) cc_final: 0.2434 (t-170) REVERT: J 79 LEU cc_start: 0.3971 (OUTLIER) cc_final: 0.3759 (pp) outliers start: 71 outliers final: 35 residues processed: 257 average time/residue: 1.0037 time to fit residues: 338.3369 Evaluate side-chains 233 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 178 SER Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain S residue 15 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 534 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 315 optimal weight: 30.0000 chunk 404 optimal weight: 1.9990 chunk 313 optimal weight: 9.9990 chunk 466 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 552 optimal weight: 3.9990 chunk 345 optimal weight: 0.0770 chunk 336 optimal weight: 30.0000 chunk 254 optimal weight: 0.8980 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 45675 Z= 0.243 Angle : 0.575 15.230 62169 Z= 0.304 Chirality : 0.046 0.230 7074 Planarity : 0.005 0.072 8019 Dihedral : 4.509 27.236 6312 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.53 % Allowed : 11.29 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 5703 helix: 1.76 (0.20), residues: 720 sheet: 1.10 (0.12), residues: 1993 loop : -0.79 (0.11), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 353 HIS 0.011 0.001 HIS C 207 PHE 0.028 0.002 PHE C 157 TYR 0.021 0.001 TYR C 265 ARG 0.005 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 203 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: A 500 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7213 (t) REVERT: A 740 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7508 (ttp) REVERT: M 82 MET cc_start: 0.2865 (pmm) cc_final: 0.2226 (pmm) REVERT: N 100 PHE cc_start: 0.3598 (OUTLIER) cc_final: 0.2060 (t80) REVERT: B 387 LEU cc_start: 0.5219 (OUTLIER) cc_final: 0.4987 (mt) REVERT: P 165 VAL cc_start: 0.1805 (OUTLIER) cc_final: 0.1574 (t) REVERT: Q 178 SER cc_start: -0.0052 (OUTLIER) cc_final: -0.0347 (t) REVERT: C 646 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7062 (ttp-170) REVERT: I 87 MET cc_start: 0.0039 (OUTLIER) cc_final: -0.0341 (pmm) REVERT: I 103 HIS cc_start: 0.2961 (t-170) cc_final: 0.2495 (t-170) REVERT: J 79 LEU cc_start: 0.4028 (OUTLIER) cc_final: 0.3811 (pp) REVERT: S 128 LYS cc_start: 0.2070 (pmtt) cc_final: 0.1535 (mppt) outliers start: 77 outliers final: 41 residues processed: 261 average time/residue: 0.9833 time to fit residues: 338.7852 Evaluate side-chains 237 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 178 SER Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain S residue 15 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 341 optimal weight: 10.0000 chunk 220 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 106 optimal weight: 30.0000 chunk 351 optimal weight: 20.0000 chunk 376 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 434 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN C 207 HIS ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 45675 Z= 0.504 Angle : 0.714 13.367 62169 Z= 0.381 Chirality : 0.053 0.252 7074 Planarity : 0.006 0.075 8019 Dihedral : 5.128 33.670 6312 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.87 % Allowed : 11.59 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 5703 helix: 1.08 (0.19), residues: 730 sheet: 0.85 (0.12), residues: 2025 loop : -0.97 (0.11), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 353 HIS 0.012 0.002 HIS C 207 PHE 0.034 0.003 PHE C 157 TYR 0.028 0.002 TYR C 265 ARG 0.011 0.001 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 207 time to evaluate : 3.701 Fit side-chains revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8340 (mm) REVERT: M 82 MET cc_start: 0.3046 (pmm) cc_final: 0.2482 (pmm) REVERT: N 100 PHE cc_start: 0.3862 (OUTLIER) cc_final: 0.2224 (t80) REVERT: H 87 MET cc_start: 0.3170 (mmm) cc_final: 0.2771 (mmp) REVERT: B 387 LEU cc_start: 0.5378 (OUTLIER) cc_final: 0.5037 (mm) REVERT: B 740 MET cc_start: 0.7958 (ttt) cc_final: 0.7710 (ttt) REVERT: Q 178 SER cc_start: 0.0135 (OUTLIER) cc_final: -0.0176 (t) REVERT: E 117 MET cc_start: 0.1398 (OUTLIER) cc_final: 0.0404 (ppp) REVERT: C 513 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7722 (mp) REVERT: C 646 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7080 (ttp-170) REVERT: I 87 MET cc_start: 0.0193 (OUTLIER) cc_final: -0.0319 (pmm) REVERT: I 103 HIS cc_start: 0.2973 (t-170) cc_final: 0.2531 (t-170) REVERT: S 128 LYS cc_start: 0.1973 (pmtt) cc_final: 0.1363 (mmpt) outliers start: 94 outliers final: 52 residues processed: 279 average time/residue: 1.0020 time to fit residues: 369.2960 Evaluate side-chains 246 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 178 SER Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain S residue 15 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 502 optimal weight: 20.0000 chunk 529 optimal weight: 2.9990 chunk 482 optimal weight: 0.7980 chunk 514 optimal weight: 5.9990 chunk 528 optimal weight: 10.0000 chunk 309 optimal weight: 0.4980 chunk 224 optimal weight: 1.9990 chunk 404 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 465 optimal weight: 4.9990 chunk 486 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 450 ASN ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 45675 Z= 0.221 Angle : 0.577 11.565 62169 Z= 0.306 Chirality : 0.045 0.194 7074 Planarity : 0.005 0.076 8019 Dihedral : 4.631 27.718 6312 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.35 % Allowed : 12.42 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 5703 helix: 1.70 (0.20), residues: 718 sheet: 0.98 (0.12), residues: 1992 loop : -0.84 (0.11), residues: 2993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP N 35 HIS 0.012 0.001 HIS C 207 PHE 0.028 0.001 PHE C 157 TYR 0.034 0.001 TYR P 110 ARG 0.006 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 200 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: M 82 MET cc_start: 0.2783 (pmm) cc_final: 0.2036 (pmm) REVERT: N 100 PHE cc_start: 0.3731 (OUTLIER) cc_final: 0.2080 (t80) REVERT: H 2 ILE cc_start: 0.3736 (pt) cc_final: 0.3280 (mt) REVERT: H 87 MET cc_start: 0.2993 (mmm) cc_final: 0.2744 (tpp) REVERT: H 108 ASN cc_start: 0.4695 (m-40) cc_final: 0.4427 (m-40) REVERT: Q 178 SER cc_start: 0.0033 (OUTLIER) cc_final: -0.0291 (t) REVERT: C 207 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.6962 (t-90) REVERT: C 646 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7034 (ttp-170) REVERT: I 87 MET cc_start: 0.0114 (OUTLIER) cc_final: -0.1497 (tpp) REVERT: I 103 HIS cc_start: 0.2938 (t-170) cc_final: 0.2675 (t-170) REVERT: J 79 LEU cc_start: 0.3986 (OUTLIER) cc_final: 0.3748 (pp) REVERT: S 128 LYS cc_start: 0.1809 (pmtt) cc_final: 0.1495 (mppt) REVERT: S 209 LYS cc_start: 0.0304 (tptm) cc_final: -0.0738 (tptp) outliers start: 68 outliers final: 48 residues processed: 251 average time/residue: 0.9723 time to fit residues: 322.7088 Evaluate side-chains 240 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 178 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain S residue 15 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 512 optimal weight: 9.9990 chunk 337 optimal weight: 8.9990 chunk 544 optimal weight: 8.9990 chunk 332 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 378 optimal weight: 9.9990 chunk 570 optimal weight: 20.0000 chunk 525 optimal weight: 40.0000 chunk 454 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 351 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 955 ASN A1135 ASN ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B1010 GLN B1135 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 779 GLN I 103 HIS ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.177 45675 Z= 0.780 Angle : 0.876 11.648 62169 Z= 0.470 Chirality : 0.062 0.323 7074 Planarity : 0.007 0.078 8019 Dihedral : 5.718 38.472 6312 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.57 % Allowed : 12.54 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 5703 helix: 0.41 (0.18), residues: 735 sheet: 0.53 (0.12), residues: 2018 loop : -1.23 (0.11), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 353 HIS 0.050 0.002 HIS C 207 PHE 0.038 0.004 PHE C 898 TYR 0.036 0.004 TYR C 265 ARG 0.013 0.001 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 196 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 69 LEU cc_start: 0.1628 (OUTLIER) cc_final: 0.1248 (tp) REVERT: Q 178 SER cc_start: 0.0664 (OUTLIER) cc_final: 0.0200 (t) REVERT: C 513 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7714 (mp) REVERT: C 646 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7090 (ttp-170) REVERT: I 87 MET cc_start: 0.0198 (OUTLIER) cc_final: -0.1488 (tpp) REVERT: S 128 LYS cc_start: 0.2038 (pmtt) cc_final: 0.1578 (mppt) outliers start: 79 outliers final: 55 residues processed: 259 average time/residue: 0.9957 time to fit residues: 340.8615 Evaluate side-chains 244 residues out of total 5037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 178 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain S residue 15 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 278 optimal weight: 5.9990 chunk 361 optimal weight: 6.9990 chunk 484 optimal weight: 0.7980 chunk 139 optimal weight: 20.0000 chunk 419 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 455 optimal weight: 0.7980 chunk 190 optimal weight: 40.0000 chunk 467 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 HIS C 207 HIS I 103 HIS ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.230466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.214642 restraints weight = 75533.030| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 1.10 r_work: 0.4270 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.4202 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work: 0.4089 rms_B_bonded: 3.77 restraints_weight: 0.1250 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45675 Z= 0.197 Angle : 0.590 11.385 62169 Z= 0.312 Chirality : 0.045 0.195 7074 Planarity : 0.005 0.077 8019 Dihedral : 4.773 26.364 6312 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.09 % Allowed : 13.28 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 5703 helix: 1.52 (0.20), residues: 727 sheet: 0.78 (0.12), residues: 2023 loop : -0.95 (0.11), residues: 2953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 35 HIS 0.015 0.001 HIS I 103 PHE 0.027 0.001 PHE B 541 TYR 0.032 0.001 TYR P 110 ARG 0.008 0.000 ARG N 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8819.36 seconds wall clock time: 156 minutes 21.55 seconds (9381.55 seconds total)